Secretary-General of the Indonesian Red Cross Iyang Sukandar said all the bodies had been wearing civilian clothes, but this did not necessarily mean they were civilians.
"We cannot determine their identities. Our job is to evacuate the bodies to hospitals," Sukandar said.
The revelation comes as a state-controlled human rights investigator said a mass grave had been found near Bireun in the war-torn province.
"That grave is confirmed, yes, but what happened, the number of victims and the witnesses hasn't yet been (confirmed)," MM Billah, of the Indonesian National Commission on Human Rights said.
Earlier, the commission which sent a fact-finding team to Aceh reported a variety of rights abuses. These included the burning of almost 500 schools, summary killings, arbitrary arrests, the torture of unarmed civilians, sexual harassment and forced displacement.
But team leader Billah did not say who was responsible for the abuses. He said a follow-up team would be sent.
Billah said the team obtained information that armed groups recruited from non-Acehnese civilians had been supporting the military offensive.
The Indonesian military has said 175 rebels had been killed, as of Wednesday, along with 24 soldiers and four policemen. The military concedes the death of 18 civilians. It says more than 300 rebels are under arrest.
Monitors told to leave
Meanwhile, a military spokesman said troops were pursuing separatist rebels after a bloody ambush which cost the lives of seven soldiers.
Martial law administrator Major General Endang Suwarya said the Swiss-based international mediators, the Henry Dunant Centre, should quit the province immediately. The Dunant Centre brokered a peace deal that lasted five months, but it gradually fell apart.
Indonesia also announced it would ban foreign tourists from Aceh and review the presence of non-governmental organisations and foreign journalists for their own safety.