John Aglionby, Banda, Aceh – After only a week of its offensive against the Free Aceh Movement (GAM), which military commanders promised would end in the separatists' elimination, Indonesia yesterday conceded it would never defeat the rebel army.

The surprising admission came as the security forces extended to students their crackdown on opposition to the war, with paramilitary police arresting at least 15 people, including Red Cross volunteers and refugees, in a raid on a students' union.

Indonesia's chief military spokesman, Major General Sjafrie Sjamsuddin, said that in "an unconventional operation such as a guerrilla war, no one can eliminate [the enemy] until the last personnel".

The armed forces chief, General Endriartono Sutarto, said last week it was hoped GAM would be crushed within six months. Gen Sjafrie said: "When [Gen Sutarto] said 'crush them to their roots', he meant we can reduce their personnel [and] cut off their lines of command and logistics. We are facing difficulties because GAM are melting into the community. They are taking off their uniforms and hiding their weapons." He denied reports that the 45,000 troops and police were deliberately harming civilians but promised all alleged atrocities would be investigated.

"We have difficulties distinguishing between GAM and civilians. We cannot [guarantee] a zero casualty rate. But it's not on purpose." Events on Saturday night at the State Islamic Institute appeared to belie this. Police said they raided university accommodation and arrested 17 separatists. A police commander, Sayed Hussain, said those held were "probably political members or from clandestine movements [linked to GAM]".

Students who said they witnessed the raid, which they said was a two-hour violent attack on the students' union and not on accommodation, said 15 people were arrested and that none of them was connected to separatists.

"Three of the students were Red Cross volunteers, five were from the environmental society, one was just an ordinary student and two were from the university regiment," said Abdillah, who was hiding in a nearby building.

"We heard the beatings and screaming so we just kept as quiet as we could." The students' version is given credibility by the fact that when the Guardian visited the students' union yesterday morning, most of the eight rooms in it had clearly just been vandalised.