The Polish Church was hit by its most serious crisis since the fall of Communism when the new Archbishop of Warsaw resigned minutes before his planned inaugural Mass, admitting collaboration that he had previously denied. Only openness and humility can begin to repair the damage

The ugly scenes that erupted outside Warsaw Cathedral last Sunday after what was to have been the installation of a new archbishop revealed the tensions now afflicting Poland's Catholic Church. In the war of words over the resignation of Archbishop Stanislaw Wielgus, everyone has been diminished: the bishops who tried to force his appointment through despite confirmation of his past links to the secret police; the Vatican officials who were made to look incompetent and ill-informed; and the many ordinary Catholics left embittered by the baying of the accusers matched by the high-handedness of their pastors.

What is certain is that grave errors were committed, which were compounded by a tangled web of evasions and half-truths. In April 2005, the death of John Paul II exposed a vacuum of leadership in Poland, which has widened and deepened since. With its façade of unity and uniformity now shattered, the Church's image has been badly damaged.

With wise handling, this could be a moment of catharsis, a chance to shake off the fusty, authoritarian attitudes of the past. Poles are religious people. There will be no emptying of pews or turning of backs. But the scandal surrounding Archbishop Wielgus has exposed a culture of arrogance and secrecy, and raised serious questions about power and authority in the Church. From the start of 2007, Polish Catholicism cannot be the same.

The Church's prestige in Poland is largely built on its Communist-era defence of human rights and national independence. There was, however, another darker side that was little talked about. Around one in 10 Catholic clergy are estimated by the official National Remembrance Institute to have informed for the secret police, known as the Sluzba Bezpieczenstwa, or SB. However, virtually all were approached at one time or another, especially those with particular needs and vulnerabilities, with highest recruitment rates in the 1980s during the struggle with the Solidarity movement.

Reports that the name of the then Bishop Wielgus, a former rector of the heavily infiltrated Catholic University of Lublin, had been found in SB files surfaced when his candidacy for the Warsaw archdiocese was mooted in early November and were promptly ridiculed. As Bishop of Plock and vice-chairman of Poland's Church-State Joint Commission, the former academic had his critics. In a statement before autumn's local elections, he accused politicians of using slogans to camouflage their "egotistic interests" and urged voters to back "honest, law-abiding, wise and competent people" over "careerists prone to corruption". Asked about the vetting of clergy agents, he said he was irritated by "ahistorical views which ignore Communist-era realities", adding that his Plock diocese had lacked "specialists" to mount its own archive enquiries. He also attacked the "new Left" and the "religious illiteracy" of Polish Catholics, and backed calls to have religious teaching introduced for sixth-formers and an abortion ban written into Poland's constitution.

Views like these placed Wielgus firmly on the side of conservative, anti-reformist clergy, whose position has been championed by Poland's controversial Redemptorist-run Catholic broadcaster, Radio Maryja. It was, predictably, from this quarter that the most vociferous support came when his nomination was confirmed on 6 December.

When the Gazeta Polska weekly named Bishop Wielgus a few days before Christmas as a "trusted collaborator" of the SB, church leaders dismissed the claims out of hand. "The mere fact that a priest had talks with Communist security service employees cannot be taken as proof of immoral collaboration," the Bishops' Conference said in a statement, urging Catholics to respect the Pope's appointment. The accusations were also rejected by a Vatican press office communiqué, which insisted Benedict XVI had "full confidence" in the new archbishop and had taken account "of all his life circumstances, including those connected with his past". Even when the archbishop's 88-page file was published on the internet in early January, and the incriminating evidence confirmed by the Church's own commission, Archbishop Wielgus' supporters appear to have concluded that they could still face down the accusers.

Having adamantly denied the charges, the new archbishop finally admitted meeting SB agents on numerous occasions, and signing a pledge of collaboration during a "moment of weakness" in 1978. However, in a statement three hours before taking office on 5 January, he defended his actions and rejected the "falsifications" and "insinuations" directed against him. The Pope and Vatican dicasteries had been informed, Wielgus told Warsaw Catholics in a "statement of penance" later the same day, in which he confessed to lacking the "prudence, courage and determination" to sever his SB contacts. "Today, I state with full conviction that I didn't inform on or try to harm anyone. But through this entanglement, I harmed the Church," the archbishop went on. "I harmed it again when, in recent days, facing a heated media campaign, I denied the fact of my cooperation. This weakened the credibility of statements by people of the Church, including those bishops who were in solidarity with me."

Despite this, he said he looked forward "with great joy" to serving as Warsaw metropolitan, and asked local Catholics to accept him "with a contrite heart".

Wielgus supporters, like Archbishop Slawoj Glodz of Warsaw-Praga, have insisted his service to the Church outweighs his murky past, and that unreliable secret police documents, compiled through fear and blackmail, should not be used for grave accusations. The media, they say, should go after the real SB villains, many now in comfortable retirement, instead of forming an unholy alignment with the Church's liberal and ex-Communist enemies.

Critics say these arguments, however reasonable, are irrelevant. Besides knowingly and willingly collaborating for personal gain, Archbishop Wielgus concealed his past, and repeatedly lied about it as evidence mounted against him, hitting out unjustly and self-servingly at his accusers. He allowed his appointment to go forward, knowing the consternation and division it was causing, and only resigned under pressure within hours of his ceremonial installation.

There is also disquiet about the Church's lack of openness on the subject of SB informers from the beginning. During the 1990s, Church leaders were urged to pre-empt possible damage by researching the archives themselves, before they could be seized on by enterprising journalists and academics. They showed little inclination to do so.

In a long-awaited report last August, the Bishops' Conference insisted the "decisive majority" of Catholic priests had proved "worthy servants of Christ" under Communist rule, in some cases paying with their lives. Those who had acted as SB informers would have to declare their guilt, apologise and make reparations. The Church would urge "a cleansing of memories through conversion and penance" rather than through condemnations.

Many Catholics believe the hierarchy has continued to stall, calculating that public opinion will lose interest or be prevailed upon to drop the issue, and that less damage will be done by complaints of evasion than by transparent investigations. Although a Church commission was announced in the report, it took till October to appoint its members, and till December to hold its first meeting. Several dioceses and religious orders have set up their own teams in the meantime. But none of these has submitted any findings. Meanwhile, independent enquiries have been discouraged and in some cases suppressed.

Lay Catholics and media editors who helped bring the Wielgus affair to light deserve an apology, after being accused of malice and dishonesty by the bishops, and denounced as "death squads" by Radio Maryja, which bussed its supporters to Sunday's aborted installation. Those who damaged the Church's credibility with further denials should be called to account. The Church's critics praise the example shown by Bishop Wiktor Skworc of Tarnow when his name was also found in SB files last November. The bishop promptly asked a group of historians to check the material and was quickly exonerated. The Church's reputation can be rebuilt, but only if it confronts failures openly.

Although Archbishop Wielgus' departure should have pointed to a solution, there are signs that the tensions could worsen before they heal. Some Catholics say the atmosphere was exacerbated by an ill-judged weekend statement by the Vatican's Jesuit spokesman, Fr Federico Lombardi, blaming attacks on the Polish Church on a "desire for revenge", and by Cardinal Glemp's hastily composed Warsaw Cathedral homily, which appeared to question the Pope's judgement. "The Church has other qualifying categories than the crystally pure past of a candidate," said the cardinal, who is to remain as Poland's Catholic Primate until he turns 80 in three years' time. "Today, a judgement has been made on Archbishop Wielgus - and what a judgement! - on the basis of scraps of paper, documents copied three times. We don't want such judgements."

Questions are being posed about the Church's relations with Poland's centre-right Government, whose commitment to "lustration", or the screening of former agents, has been a key policy. They are also being asked about the Church's loyalty to the Pope, who was said this week to be "extremely angry" about the way his authority was exploited and jeopardised by the archbishop's supporters.

Meanwhile, Poland's Media Ethics Council has apologised to the Gazeta Polska weekly for accusing it of "abusing free speech" and says it now accepts the pre-Christmas report which initiated the crisis was "dictated by courage and responsibility for the common good". It seems unlikely that anyone in Poland will be able to bring the various sides together. Whoever eventually does will have to unravel the truth and apportion responsibility for the disastrous turn of events; to reassure public opinion that the Church is committed to proclaiming the Gospel rather than defending its corporate interests; and to set it on a new path of tolerance and fairness, in which everyone possesses equal rights and dignity and differences of opinion are respected.