Prime Minister Benjamin Netanyahu said the remarks were "unacceptable" while other politicians and LGBT rights groups also voiced criticism.
The Aguda, an LGBT rights non-profit organisation, called for Mr Peretz's resignation.
During Saturday's interview Mr Peretz also described his response when a man told him he was gay.
"First of all, I embraced him. I said very warm things to him. I told him, 'Let's think. Let's study. And let's contemplate,'" he said.
"The objective is first of all for him to know himself well... and then he will decide."
Mr Netanyahu added: "The education minister's remarks... are unacceptable to me and do not reflect the position of the government that I head."
The prime minister said he had spoken to Mr Peretz, a leading member of the ultranationalist United Right alliance, to emphasise his criticism.
Nitzan Horowitz, who leads the left-wing Meretz party, said conversion therapy was a dangerous practice which causes "extremely severe circumstances for youths, including suicide".
