Boim caused outrage on Wednesday when he suggested Palestinian killings of Israelis could only be explained by a "genetic defect".
He was speaking at a memorial service for 37 passengers killed on a bus by a Palestinian resistance bomber on 11 March 1978 north of Tel Aviv.
"Of course I never thought of such a thing, and it was a slip of the tongue," Boim told national radio.
But it is not the first time Boim has made a comment he was later forced to publicly regret.
Last October, the deputy minister justified the killings of Palestinian civilians after Apache helicopters were used to pursue two men who had attempted to avoid a checkpoint.
Seven Palestinians died as a result of the chase in which no attempt was made to question or arrest the two alive.
"We try to act against targets in a surgical fashion, but there are at times civilian injuries … but it needs to be said that terror is also supported by the population."