Palm Sunday at Tripoli's Anglican church is normally a joyous affair, with expatriate Christians parading in the spacious front yard with traditional palm branches. Not this year.

Fearing the attention of Islamist militants after recent attacks on churches and the arrest of dozens of Christians accused of proselytising, the church cancelled last weekend's planned parade.

"We usually celebrate with pomp, but I said no," said the Rev Vasihar Baskaran, vicar of the church of Christ the King, in Tripoli's picturesque Old Town, a popular venue for British, American, African and Asian worshippers. "I thought it was better not to attract the attention of bad elements. I told the congregation: when the service is finished, don't stand in the churchyard and drink tea and have fun, just go home."

It is the same story at the nearby Catholic church of St Francis, which has closed its doors outside service hours after a uniformed gunman shot at a priest on the church steps.

Libya has no recognised Christian community, but the small collection of churches serving foreign residents are braced for trouble at this weekend's Easter services.

Earlier this month jihadist militants set Benghazi's Coptic church ablaze with the priest inside it; his life was saved by local Muslim residents rushing into the flames. That followed the killing of two Egyptian worshippers in the bombing of another Coptic church in Misrata earlier this year. Tripoli's Coptic church has a 24-hour police guard; the Greek Orthodox church has closed, its priest returning to Greece after he was shot at outside his home.

Meanwhile, Libya's defence ministry has begun a crackdown on Christians accused of proselytising, beginning in February with the arrest of an American, an Egyptian, a South African and a South Korean accused of spreading Christian literature in Benghazi.

A further 48 Egyptian Copts were arrested in the same city, triggering protests and the burning of the Libyan flag in Cairo when one of the arrested died in custody.

The arrests were made by the Office of Preventive Security, a defence ministry unit tasked with defending Libya's Islamic culture.

At its military compound on the outskirts of Benghazi, preventive security commander Abdul Salam Barghathi showed off a collection of Bibles and Christian tracts in English and Arabic that he said were among 55,000 books seized in a raid on an evangelist warehouse.

"They were printing these in the city. Some of these books were given to children," he said.

Barghathi said the arrested Christians were shortly to be released as a "diplomatic gesture". "Anything that comes from abroad can be an invasion against our ideas and our thoughts, which can be a danger to homeland security," he said. "David Cameron has a famous saying. He said, 'Concerning the homeland security, don't ask about human rights'. I saw it on Facebook."

A few miles away the city's Coptic church is a blackened, abandoned ruin. Inside, wrecked furniture lies amid smashed stained glass and charred pews, reeking of smoke and rotting fruit from the ransacked kitchen.

Neighbour Abdul Muhammad said local Muslims saved the life of the priest after militants set the building ablaze. "We didn't know the priest was inside, then we heard him shouting. One of our guys took his gun and threatened to shoot anyone harming the priest, and we managed to get him out and drive him to the [Egyptian] consulate."

It is far from clear that jihadist militants enjoy widespread support; rather, they operate in a security vacuum in a country hamstrung by weak and divided government. The Benghazi church attack, like that by Islamists who killed US ambassador Chris Stevens at the American consulate in September, has triggered revulsion in a city which was the cradle of Libya's Arab spring revolution. "Trust me, the Christians are our friends, we get on with them," said Muhammad. "Our revolution was about freedom."

Meged Labib, an Egyptian Christian market trader, who showed a small blue cross tattooed on his wrist, agreed. "Really, we have no troubles with most people in Benghazi, I have Muslim friends here."

But he admitted being nervous. "Our priest fled to Egypt; I don't think they will repair the church. For now, we hold services at home."

Barghathi insisted his forces would protect churches, and condemned the militant attacks, but advised Christians not to attempt to spread their faith in Libya. "They should be careful. Anything that touches our religion offends us very badly. I don't really advise the Egyptians to get another church now."

Back in Tripoli, Baskaran insists Easter services will go ahead, albeit with the church door closed. "We will use the Easter services to pray for Libya. There is so much good in this country," he said.