BENGHAZI, Libya (Reuters) - Unknown assailants set fire to an Egyptian Coptic church in the eastern Libyan city of Benghazi on Thursday, witnesses said, the second attack on the building in weeks.

Residents said the attack appeared to be in reaction to a protest at the Libyan embassy in Cairo earlier this week where Egyptian protesters burnt a Libyan flag outside the embassy and, according to police at the scene, held aloft a cross.

The demonstrators there said they were protesting the death of an Egyptian Copt in an explosion in front of a church in Libya a month ago.

The church in downtown Benghazi was heavily damaged and charred inside, witnesses said, with bookshelves ransacked. As crowds gathered at the scene, the fire was eventually put out.

Officials said they were not aware of any injured as the church was empty when the attack happened.

"There were rumors of plans to set fire to the church. We didn't hear anything today though, we just saw the smoke billowing," one resident who gave his name as Bodelal said.

This was the second attack on the Egyptian Coptic church in Benghazi in weeks. Gunmen had previously attacked it, assaulting two priests.

About 250 gathered again in front of the embassy in Cairo on Thursday, clashing with Egyptian riot police, a security source said.

"This could be reaction against what happened at the embassy. They burnt the Egyptian flag in front the embassy," another Benghazi resident, Abdusalem Salem, said.

Libya's small Christian community has expressed fears over Islamist extremism as the government struggles to impose its authority over armed groups which have refused to lay down their weapons since the 2011 war that ousted Muammar Gaddafi.

In December, an explosion at a building belonging to a Coptic church in Dafniya, close to the western city of Misrata, killed two Egyptian men and wounded two others.

Last month, four foreigners were arrested in Benghazi on suspicion of being Christian missionaries and printing books about Christianity.

(Reporting by Ali Shuaib and Firas Busalum; Writing by Marie-Louise Gumuchian)