Reports of rebels threatening churches with firing squads, storming church services and holding pastors hostage are just some of the stories that have emerged from rebel-held regions of eastern Ukraine in recent months.

The threat to Ukraine's evangelical churches is a lesser-known aspect of the ongoing political struggle between the pro-Russian separatists and the Ukrainian government in Kiev. A fragile ceasefire was agreed on September 5, though this week the rebels have resumed attacks on Donetsk airport, a key site in the conflict, and yesterday a Red Cross aid worker was killed by shelling in Donetsk.

On Saturday, Seventh Day Adventist minister Sergei Litovchenko was abducted by pro-Russian gunmen during a church service in Horlivka, in the Donetsk region. This is just one of many reports of infringements on religious practice within the rebel-controlled eastern regions – areas now known as the Donetsk People's Republic (DPR) and the Luhansk People's Republic (LPR).

The Institute for Religious Freedom (IRF), based in Kiev, has recorded numerous incidents of religious persecution that took place in June and July. In August, Human Rights Watch reported several cases of arbitrary detention and torture, which had been largely overlooked by the media. 

In June, the IRF reported that gunmen, under the command of rebel leader Igor Girkin, captured four men from Transfiguration Evangelical Church in Sloviansk, Donetsk. The town's deputy prosecutor, who managed to escape from DPR detention, said the men had been tortured and then shot. A Ukrainian government advisor said the men had been buried in a mass grave.

Over the summer numerous churches in Donetsk had their buildings looted and occupied by pro-Russian militants.

On June 19 armed guards stormed into Word of Life Evangelical Church in Torez, Donetsk. "They ordered us to take the furniture and get out, insisting that these churches are sects and they will be destroyed. The people in the building were threatened with a firing squad if they made a fuss about the incident," pastor Segiv Kosiak told IRF.

In July the Donetsk Christian University was seized, with militants saying (according to the IRF): "Due to the military situation in the city, the Donetsk Christian University will be made available to military units of the DNR, including all property, equipment, and other supplies and those who do not obey will face court-martial."

Another Word of Life Church in Donetsk had its building taken over by the rebels on August 13. Pastor Leonid Padun wrote on his blog the following day: "There are no words to express the pain and sorrow! For over twenty years we have invested [our] hearts, our finances into the church building, and now we are deprived of the opportunity to gather for prayer and worship to God."

In September Padun wrote again to encourage his church: "I believe that these times of suffering will make us stronger in faith, refining us, changing our character, and making us more like Christ. [...] God has so much good in store for the Church, for our city and our country!"

Several incidents are recorded of church pastors and parishioners being kidnapped and detained for short periods before being released with warnings – as if the primary purpose of the exercise is to instil fear.

It is questionable whether Christians are coming under more attack than any others who disagree with the rebels. However, Oleksandr Zaiets, head of the IRF says: "Leaders of the separatist movement in Donbas [...] accept evangelical churches as those which are supposedly financed by the West for spying and closely cooperate with the US and the EU."

Many Ukrainian churches joined together during the Euromaidan protests in Kiev, which began in November last year, and have subsequently supported the Ukrainian government rather than the separatist rebels. This will no doubt increase the perception that the churches are Western-backed institutions.

"They suggest that believers who do not belong to the Moscow Patriarchate, are unreliable persons in light of the Orthodox idea of ​​Russian World and related with it doctrine of Eurasianism," Zaiets says.

"This religious and geopolitical idea was proclaimed by the head of Russian Orthodox Church in Moscow a few years ago," he adds.

It isn't only the Christians who are coming under fire. At the end of August a Jewish man, George Zillerbord, was shot dead by rebels when he tried to stop them robbing his neighbours' house. The Ukrainian Religious Information Service reports that a synagogue in Donetsk was closed down in August, adding that the Jewish community in Donetsk has "almost ceased to exist". And according to the Jerusalem Post, thousands of Jews have left Donetsk, leaving behind only about 1,000 of its pre-conflict community of around 10,000 people.

Despite acknowledging an increase in the number of Jews leaving Ukraine, the chair of the Association for Jewish Communities and Organisations in Ukraine, Josef Zisels said in a speech last month: "This war does not have a particularly Jewish side to it." He added that anti-Semitic incidents in Ukraine remained low – in fact, as low as previous years.

The religious aspect of the struggles in eastern Ukraine may currently be overshadowed by political concerns, but there are fears that it indicates a worrying pattern of events for the future.

Last week the papal diplomat to Ukraine Archbishop Thomas Gullickson issued a warning about the Greek Catholic community in the country. "There is no reason for excluding the possibility of another wholesale repression of the Ukrainian Greek-Catholic Church as came about in 1946 with the complicity of the Orthodox brethren and the blessing of Moscow," he said, at an Aid to the Church in Need meeting.

The Ukrainian Greek Catholic Church was severely persecuted during Soviet times, and the intimidation of many Christian communities currently taking pace in eastern regions is a troubling reminder of the past.