Modise, now Defence Minister, made the admission during questioning on the ANC's second submission to the TRC at a special hearing in Cape Town.
He said when the ANC leadership became aware of the problem they took immediate corrective steps, sending senior MK officials to the camps to ensure the practice was stamped out.
"Unfortunately this kind of problem is a very difficult one. It is a kind of problem that manifests itself in places such as camps that are very far from home and isolated in hostile areas."
It had been difficult for young men to go into nearby towns to look for young ladies because they risked being ambushed by Unita troops.
"The confinement of men and women resulted in these abuses."
It was also true that some camp commanders had taken advantage of their positions of authority to ask sexual favours of women in the camps.
"I think it is understood what is meant by favours," Modise told the TRC panel, chaired by Archbishop Desmond Tutu.
Commanders implicated in such practices had been removed from their posts.
ANC national executive committee member Gertrude Shope said the ANC Women's League had taken action when it heard about the abuses. A delegation had visited the various camps in Angola to meet the women and discuss their problems.
Former MK intelligence chief Ronnie Kasrils, now deputy defence minister, stressed that MK had had great respect for women.
"Any abuse of women that took place was not part and parcel of every day occurrence. This is something that would have been hidden.
"When it was brought to our attention that certain abuses were taking place behind the scenes we took action."