The fighters were killed in four separate clashes on Friday, Aceh military spokesman Ari Mulya Asnawi said on Saturday.
The killings made up one of the highest number of casualties suffered by the Free Aceh Movement in a single day since the government launched a major offensive to crush the separatists in May 2003.
An estimated 12,000 people - many of them civilians - have been killed since the Free Aceh Movement began its revolt in 1976, with rights groups accusing both Indonesian troops and separatists of widespread abuses.
Jakarta launched an operation to try to crush the rebellion after peace talks broke down in May 2003.
The military says more than 2300 separatists have been killed since then.
Rights groups however say many of the victims were civilians, a charge denied by the government.