Kyiv, Ukraine - "It wasn't a search, it was a sacrilege," Father Anatoly Kaplyuk said, describing how police and intelligence officers interrupted service in his church in the northern Ukrainian town of Ovruch.

In early December, they entered the building that belongs to Moscow-affiliated Orthodox Church, one of Ukraine's largest religious groups, to look for "materials inciting religious hatred", police said.

The searches were part of mounting pressure on pro-Russian clerics that stems from Ukrainian President Petro Poroshenko's battle to break away his ex-Soviet nation from religious subordination to Moscow Patriarch Kirill, Kremlin's ideological ally.

The officers looked everywhere - including the altar, an area no lay person is allowed to enter - and confiscated some booklets, Father Anatoly told Al Jazeera.

They then summoned him for questioning at the Ovruch office of the SBU, Ukraine's main intelligence agency. The questioning hasn't taken place yet, he said.

A dozen more pro-Russian priests throughout Ukraine have been questioned and had their churches or residencies searched as part of investigations into "treason" and "incitement of religious hatred", the SBU said.

Priests and bishops are ready to go through interrogations, arrests and trials but maintain their reputation among their parishioners. Nikolay Mitrokhin, Russian-Soviet sociologist

Several other pro-Russian priests posted videos of themselves online saying they were ready for questioning and will never sever their ties to the Russian Orthodox Church.

Within days, they were blacklisted by Mirotvorets ("Peacemaker"), an online publication with ties to security services that outs "Ukraine's enemies" from separatists in rebel southeastern provinces to turncoat officials in annexed Crimea.

"I am proud to be on that list along with the Holy Synod" of the pro-Russian church, Father Hennady Shkil, a white-bearded priest from the southern Ukrainian town of Hola Pristan told Al Jazeera.

Even pro-Moscow church's top hierarch was not spared.

In early November, a Ukrainian TV network showed what it claims to be the luxurious residence of Metropolitan Onufri, in his home village in southwestern Ukraine.

It broadcast drone footage showing several large houses, a helipad and a hangar-like structure that hides either a tennis court or a swimming pool.

Onufri has long been lambasted for his pro-Kremlin stand.

After Russia annexed Crimea in 2014 and backed pro-Russian separatists in southeastern Ukraine, he called them "brothers in faith" and bristled at Kyiv's military operation against them.

During a parliament session in May 2015 to commemorate the servicemen awarded for fighting the separatists, the entire audience stood up - except for Onufri and his frocked subordinates.

But experts say that by cracking down on pro-Russian clerics, Poroshenko's government inadvertently inspires resistance - just like Communist pressure on believers in the officially atheist Soviet Union.

"Priests and bishops are ready to go through interrogations, arrests and trials but maintain their reputation among their parishioners," Nikolay Mitrokhin of the University of Eastern Finland in Joensuu told Al Jazeera.

On January 6, President Poroshenko received a "tomos", a charter issued by Constantinople Patriarch Bartholomew, the most revered leader of the world's 300 million-strong Orthodox Christian community, ending the dependence of Ukraine's church from Moscow.

Predictably, the Moscow Patriarch condemned the move and cut ties with Constantinople.

"We are witnessing illegal meddling in the internal life of Ukraine's Orthodox Church, a rude, anti-canonical intervention in its area," Kirill said in early January.

His Patriarchate claims more than 150 million followers in Russia and the ex-USSR, although polls and experts say that only a fraction of them are observant.

Kirill coined the concept of "the Russian world", or Moscow's right to "protect" ethnic Russians outside Russia, and the Kremlin used the idea to justify its 2014 annexation of Crimea and support to separatists in southeastern Ukraine.

That's when Poroshenko came to power after a months-long popular uprising overthrew his pro-Moscow predecessor. Poroshenko pledged to make Ukraine part of the European Union and NATO and repel the Russian aggression.

But by the end of his first term, his success is as modest as his single-digit approval ratings. He made church independence part of his campaign ahead of the March 31 presidential election, in which he is widely expected to run.

"We are finally gaining spiritual independence that can be compared to the political independence," Poroshenko told a church council in late December.

His words are echoed by the so-called Church of the Kyiv Patriarchate that broke away from Moscow in the early 1990s and whose clerics mostly formed the new, Constantinople-recognised see after merging with another, smaller Orthodox sect.

"As a church, we try to be independent from Moscow not because we don't like Russia," Archbishop Yevstraty Zorya told Al Jazeera. "But we see how the Russian Empire has for centuries used the Orthodox Church in our land as a tool of imperial policy."

The pro-Ukrainian and Russia-affiliated churches share the doctrine of Greek Orthodoxy that split from Catholicism in 1054. They are equally opposed to same-sex marriages, abortions and birth control.

The Russia-affiliated church insists that its ties to Moscow are nominal and "spiritual," and that Poroshenko's government violates its own commitments to multiculturalism and religious tolerance.

Weak support

Despite growing pressure, less than 100 of about 12,000 Russia-affiliated parishes joined the new church, officials admit.

The issue keeps Ukrainians polarised - while 43 percent of them support church independence, 22 percent are firmly against it, mostly in the Russian-speaking eastern regions, according to a poll by the Kyiv-based Rozumkov Center conducted in late December.

Meanwhile, 47 opposition legislators accused Poroshenko of violating the cornerstone of any Western democracy - separation of church and state.

They complained to the Constitutional Court in mid-December about his government's violation of "religious freedoms and peace among confessions" by urging Bartholomew to recognise the independent Ukrainian church.

Some average Ukrainians are baffled by too much ado about religion as the country struggles with corruption.

"Maybe, we should be teaching our children biology, chemistry and economics," Olena Meshko, a 37-year-old bookseller, told Al Jazeera. "Instead, we're moving towards the Middle Ages."