Van der Merwe implicated himself and Vlok in the 1988 bombing of Khotso House in Johannesburg, then the headquarters of the SA Council of Churches, when he testified in support of amnesty applications by five former security policemen on Monday.
Van der Merwe also admitted to ordering the booby-trapping of handgrenades which killed eight African National Congress activists in 1986.
He told Sapa on Tuesday that he would delay applying for amnesty for the bombing and grenade incidents until he was certain he would not be accused of any further crimes.
"I would like to give all my men the opportunity to consider their own positions and whether they feel... I influenced them to undertake certain actions for which they must now apply for amnesty.
"If so, I would expect them to go to their attorneys and for their attorneys to contact me and say that as far as their client is concerned, I must accept responsibility.
"From the outset I have said I will accept responsibility and accountability for these actions which transpired as a result of instructions that were given by me."
Van der Merwe said he would wait and see if former colleagues came forward to implicate him in further human rights abuses. "You can only apply for amnesty once," he explained.
In an interview with Sapa, Vlok also confirmed he would seek amnesty for the Khotso House bombing, but not immediately.
"I am going to wait and see what happens. I am busy preparing my amnesty application now. It is being handled by my attorney."