Muslim militants still controlling part of the Lower Shebelle Region of Somalia have jailed and tortured a Christian for converting from Islam, sources said.

According to a story by Morning Star News, Al Shabaab rebels seized Hassan Gulled, 25, on March 23 in Bulo Marer near Qoryoley District, they said.

Gulled, who had fled to Kenya in 2007 in search of safety and a better life, had left Kenya on February 27 to visit family in Somalia, sources said.

Gulled is one of dozens of Somali refugees in Kenya facing dangers from Al Shabaab extremists as they return to Somalia following the establishment of a new government in Mogadishu and the weakening of Al Shabaab, which once held large portions of territory.

Morning Star News said as Gulled was only visiting family in Somalia, his wife remained in an undisclosed city in Kenya. Al Shabaab extremists in Kenya who knew of his Christian activities there apparently contacted members of the militant group in Somalia, who monitored his movement for three weeks before seizing him, sources said.

"Four masked, armed militia from Al Shabaab took Gulled into a Land Cruiser and then drove away as family watched him helplessly," Morning Star News reported one source said.

Another source said it was confirmed that Gulled has been jailed in Bulo Marer.

"The Al Shabaab have been torturing him to see whether he would deny his Christian faith," the source said. "Since last week, no information has surfaced concerning Gulled. There is a possibility that he could have been killed."

A militant Islamist group with ties to Al Qaeda, Morning Star News said Al Shabaab has a base in Bulo Marer, about 50 miles from Mogadishu.

Last week, however, Somali government troops backed by African Union Mission in Somalia (AMISOM) forces had reportedly taken control of nearby Qoryoley.

Morning Star News said Al Shabaab has vowed to rid Somalia of Christians, who meet secretly due to persecution. Besides Al Shabaab, the government and many in Somali society also view leaving Islam as deserving of death.

Gulled became a Christian in Kenya in 2010. He married there in 2011 and has no children.

"Gulled's wife is very distressed and worried that she might not see her husband again," Morning Star News reported a source said.

Many Somali members of Christian fellowships in Kenya have returned to Somalia after formation of a Somali government on August 20, 2012, which replaced the Transitional Federal Government, said the source, who requested anonymity.

"Several Christian agencies are helping them settle," Morning Star News reported he said. "But we are worried that some of our members are being monitored closely by Islamic extremists."

Al Shabaab has lost control of several areas of Somalia since Kenyan military forces helped to dislodge them in the past year, but they are suspected in the shooting death of a Christian pharmacist on the outskirts of Kismayo in February.

Morning Star News said two masked men killed Ahmed Ali Jimale, a 42-year-old father of four, on February 18 as he stood outside his house in Alanley village.

On December 8, 2012 in Beledweyne, 206 miles north of Mogadishu, gunmen killed a Christian who had been receiving death threats for leaving Islam. Two unidentified, masked men shot Mursal Isse Siad, 55, outside his home, Muslim and Christian sources said.

Morning Star News said Siad and his wife, who converted to Christianity in 2000 according to a source who used to worship with them, had moved to Beledweyne from Doolow eight months before. That was after Somalia's transitional federal government and African Union Mission in Somalia troops captured Beledweyne from Al Shabaab rebels.

Morning Star News said the area was under government control and there was no indication that the killers belonged to the Al Shabaab rebels who have vowed to rid the country of Christianity, but the Islamic extremist insurgents were present in Buulodbarde, 12 miles away. Christians believed a few Al Shabaab rebels could have been hiding in Beledweyne.

In the coastal city of Barawa on November 16, 2012, Al Shabaab militants killed a Christian after accusing him of being a spy and leaving Islam, Christian and Muslim witnesses said. The extremists beheaded 25-year-old Farhan Haji Mose after monitoring his movements for six months, sources said.

Morning Star News said Mose drew suspicion when he returned to Barawa, in Somalia's Lower Shebelle Region, in December 2011 after spending time in Kenya, according to underground Christians in Somalia.

Kenya's population is nearly 83 per cent Christian, according to Operation World, while Somalia's is close to 100 per cent Muslim.