A leading Greek bishop has warned lawmakers that they risk incurring the wrath of God – and will be excommunicated – if they vote in favour of legalising same-sex partnerships.

In a letter lambasting homosexuality as "an insult to God and man", the Metropolitan of Piraeus, Seraphim, pleaded with the country's deputy prime minister, Evangelos Venizelos, not to condone gay unions.

"I beseech you from the heart not to proceed," he wrote.

"You will deny yourself the blessing of the most just Lord whose help and protection we daily need as much personally as nationally … during these critical times for our country."

Last week, the 57-year-old former monk, a prominent personality in Greece's powerful Orthodox church, threatened to excommunicate any MP who endorsed civil unions among gay couples following condemnation of Athens's failure to do so by the European court of human rights.

"For the church fathers, homosexuality is the most disgusting and unclean sin," he railed in a nine-page missive made public last week. "[Such relationships] are an insult against God and man … an unnatural aberration not even observed in animals."

The cleric's stance, which opens a new front in the crisis-plagued country's often strained relations with the EU, comes days after the Strasbourg-based tribunal ruled that Athens was in violation of the European convention on human rights. Although Greece has passed legislation recognising civil partnerships among couples of opposite sexes it remains the only EU country apart from Lithuania to refuse to extend that right to same-sex couples.

Venizelos, whose socialist Pasok is the junior party in a conservative-dominated coalition, vowed to press ahead with legislation recognising the partnerships after rightwingers, taking fright at the bishop's threat, withdrew their support for the amendment in a draft anti-racism bill before the Greek parliament.

Echoing widespread criticism of the bishop, the socialists' spokesman, Dimitris Karydis, likened his tactics to those of the Taliban, insisting that Pasok would not only seek to pass the measure but, if need be, also take on the nation's influential church.

"The bishop has to tone down his rhetoric and change position just as he did with the issue of Golden Dawn," he said, referring to Greece's neo-fascist party, which supported by Seraphim succeeded in stopping an Athens theatre company from performing Corpus Christi last year. The play, by Terrence McNally, depicts Jesus Christ as being gay.

But in one of Europe's most socially conservative countries, where sex education is still not taught in schools – and where no major personality or politician has ever been bold enough to come out – that, say activists, is a big ask.

"The ruling has been a terrific victory. In the absence of any public discussion of sexuality it is a huge step against all the odds. We can see just how revolutionary it has been by the reaction of the church," said Grigoris Valianatos, a veteran gay activist who first brought the case to the court in 2009. "Modern Greece remains deeply homophobic," he told the Guardian. "It is clear the conservatives are fishing for votes in Golden Dawn's camp and that will make change even harder."

The Holy Synod, the church's governing body, has announced it will convene next week to debate the issue. "Our position is well-known," said its spokesman Father Timotheos. "We are against such things."

Recently, the church has been hit by a series of scandals often involving priests in lewd acts with other men – including one being photographed posing in a wedding dress and fur. They, too, are expected to be on the synod's agenda but Father Timotheos refused to be drawn on the subject.