A secret Soviet-era document uncovered in Estonia suggests that Patriarch Alexy II, the head of the Russian Orthodox Church and spiritual leader of tens of millions of Christians, was a fully fledged KGB agent.

Accusations that Alexy, elected Patriarch in 1990, co-operated closely with the KGB under the code name 'Drozdov' (Thrush), have circulated since a parliamentary commission was allowed a brief peek at secret police files in Moscow in 1991.

But the Estonian text is the first publicly available document to support the theory that Alexy was more than a mere collaborator and that from 1958 he was an active agent, using the KGB as a career ladder at a time when the secret police persecuted organised religion.

The Russian Orthodox Church claims the document is a forgery but has made no attempt to disprove its authenticity. The Patriarch has made no comment.

'As far as I understand, what's being said is that someone, somewhere, brought out into the open some kind of paper carrying neither the Patriarch's signature nor reliable information that he had any kind of involvement in this sort of activity,' said a Church spokesman, Father Vsevolod Chaplin.

Yet the evidence, in the 1958 annual report of the Estonian branch of the KGB, which was left behind in Tallinn when the Soviet authorities pulled out of the newly independent country in 1991, is compelling.

The report, seen by the Guardian, consists of a stack of yellowing typewritten pages bound together as a book, which carries the legend 'Top Secret Ekz. No. 2 Series K' and the title `Summary of operational intelligence work by the 4th department of the KGB in the Council of Ministers of the Estonian SSR in 1958'.

On page 125 is a short account of the recruitment, in that year, of a young Orthodox priest given the codename 'Drozdov'. The agent is not named, but key characteristics coincide with Alexy's life.

Like the Patriarch, Drozdov was born in Tallinn in 1929, spoke fluent Russian and Estonian, was a doctor of theology and was serving as an Orthodox priest in Estonia in 1958.

Drozdov, who impressed the KGB with his eagerness, discretion and lively, forthcoming manner, began his career as an agent by providing information on a corrupt priest at a church in the small town of Jyhvi.

The Patriarch was the rector of the Church of the Epiphany in Jyhvi from 1950 until 1957. By 1961 he had become the bishop of Tallinn and Estonia aged only 32. The 1958 KGB report on Drozdov said his promotion to this post was 'considered' during his recruitment.

In the same year that he became a bishop, Alexy's rapid rise within the World Council of Churches began - the very course the KGB planned for Drozdov.

Indrek Jurjo, the Estonian historian who investigated the KGB report, said: `It must be him. It's very close. There were very few priests of the Orthodox Church here at that time. The description, the age, the plan for him to become a bishop - it fits.'

The report describes Drozdov as agreeing to work for the KGB on patriotic grounds. 'He's described here as an agent,' said Mr Jurjo. 'That means he had a KGB officer who he met with regularly in clandestine locations and who interrogated him. He would also have written reports.' Drozdov's reports, along with the KGB annual summaries after 1958, were taken to Moscow in 1991. After the 1991 putsch, President Boris Yeltsin gave a Russian parliamentary commission carte blanche to probe into some of the darkest secrets of the KGB, only to withdraw it a few months later under pressure from the secret police and other powerful figures.

Father Gleb Yakunin, an Orthodox priest and former MP who searched through KGB files, said he found several references to Drozdov. To his regret, he made no copies, and never found the card-index in which the codenames of agents were matched with their true identities.

One reference in the report from October 1969 reads: 'Agents Drozdov and Peresvyet travelled to England as part of the delegation to the Conference of European Churches.' Father Gleb, who was imprisoned in Soviet times for his opposition to state interference in the Church, said the Patriarch must lead the clergy in mass repentance.

'To co-operate with a state which sets as its aim the destruction of religion is a great sin, and a betrayal of Christianity,' he said.

The Patriarch is highly influential: the Kremlin values his support, and Alexy is close to at least one of Boris Yeltsin's likely successors, Moscow's mayor, Yuri Luzhkov.

In Russia only one small newspaper, the weekly Novaya Gazeta, has reported the Estonian find. A freelance television journalist, Boris Sobolyev, who travelled to Tallinn to film the story, has been unable to find a Russian news programme willing to air it.

Father Chaplin said: 'In recent times many anonymous photocopies of all sorts of pieces of paper have been circulated. In none of them is there the slightest evidence that the individuals we are talking about knew that these documents were being drawn up, or gave their consent. So I don't think any reasonably authoritative clerical or secular commission could see these papers as proof of anything.'