Armenia’s liberal government has never been an ally of the deeply conservative Armenian Apostolic Church (AAC), but when Prime Minister Nikol Pashinyan made extraordinary allegations against an unnamed senior clergyman, it blew open a deep divide.

“Your Grace, go fool around with your uncle’s wife. What do you want from me?” said Pashinyan.

He also accused the supreme spiritual leader – Catholicos Karekin II – of breaking his vow of celibacy and fathering a child, calling on him to resign. The BBC has approached the Church for comment but has not had a response.

Until now the Church and government had found a way to co-exist, but the row threatens to split an already polarised Armenian society still further – and affect the outcome of next year’s election.

It could also harm peace talks that have the potential to re-shape the entire region of the South Caucasus, after Armenia’s bitter defeat in a war against Azerbaijan.

Armenia is believed to be the first nation to make Christianity the state religion, after its king was baptised in 301AD. Although there is a separation of Church and state by law, the Armenian constitution recognises the AAC “as a national Church”.

The Church has not addressed the allegations but said the prime minister had sought “to silence its voice”. It has reiterated that the government has no say in the matters of Church governance.

If true, Pashinyan’s allegation would make the Catholicos unfit for office. Under the Church’s by-laws, only monks who took a vow of celibacy can be elected a Catholicos.

On these grounds Pashinyan now demands Karekin’s resignation, despite having no jurisdiction over the Church. He has presented no evidence but threatened to release it.

Pashinyan has also attacked other senior clergymen, including accusing one archbishop of having an affair, with the extraordinary allegation of “fooling around” with his uncle’s wife.

The opposition parties and two of Armenia’s former presidents, Levon Ter-Petrossian and Serzh Sargsyan, have rallied behind the Church and condemned Pashinyan’s move against it.

The government’s relationship with the Church deteriorated after the defeat in the 2020 war against neighbouring Azerbaijan, when Karekin II joined calls from various political factions for the prime minister to step down.

Pashinyan stayed in power, and the Church became a prominent anti-government voice.

Recently, Karekin II demanded the right of return for the Armenians who fled Nagorno-Karabakh, a region of Azerbaijan that it recaptured in 2023.

The prime minister’s allies are unhappy with such interventions, as they contradict the government’s position in the ongoing peace talks.

Pashinyan pushes for a swift peace treaty that would see both countries drop mutual claims. But Azerbaijani media seized on nationalist opposition demands as proof that Armenia is not ready for peace.

The Armenian Church has benefited from becoming a hub for dissent. With personal rivalries between the leaders of opposition parties, it is drawing in those disaffected with the authorities.

Political analysts in Armenia suggest this might be a real reason for the government’s sudden attack on the Church leader.

The next general election has been scheduled for June 2026, and the anti-Church campaign could be a pre-emptive strike against the stronghold of conservative opposition.

The prime minister himself has linked his position to politics: “We returned the state to the people. Now we must return the Church to the people.”

When a powerful benefactor spoke out in support of the Church this week, the government swiftly moved against him.

Russian-Armenian billionaire Samvel Karapetyan threatened to “intervene in the campaign against the Church in our own way” if opposition politicians failed to defend it.

Hours later, his residence was raided and on Wednesday he was charged with “making public calls to overthrow the government”. He denies the charge.

The conflict between Armenia’s political and spiritual leader is a highly sensitive matter far beyond its national borders, as the Church has hundreds of parishes in the diaspora, from Russia and Ukraine to Western Europe, the Middle East and America.

While rumours about Karekin’s alleged secret family have long circulated in tabloids, for years more serious accusations were being made by diaspora parishes.

They alleged that Church leaders were extorting monthly payments and micro-managing dioceses that used to enjoy operational autonomy.

In 2013, the Armenian Patriarch of Jerusalem accused Karekin II of having no spiritual values and only tending to its material wellbeing. The Church said the allegations were false.

Until recently, Nikol Pashinyan has largely stayed above the fray. “It is my belief that government has no place in the Church’s internal issues,” he said soon after taking office in 2018. After years of respecting this pledge, the prime minister might have changed his mind.

Whatever the outcome of this row, it is likely to deepen polarisation in a society that has already been fractured, not just by political infighting, but by wedge issues over whether to be allied to Russia or the West and by tensions between the residents of Armenia and ethnic Armenians from Nagorno-Karabakh.