Omurbek Tekebaev said in a written statement that he was leaving voluntarily.
Speaking to parliament today, Tekebaev said he preferred to resign rather than to apologize for the comments he made about President Kurmanbek Bakiev.
"Sorry, I have preferred to resign than to apologize," he said. " I didn't beg pardon from anybody. I wouldn't apologize for the truth."
There were calls for Tekebaev to step down after an independent television channel aired comments by Tekebaev in which he referred to Bakiev as quote "a dog" and suggested the president "hang himself from the first tree."
Tekebaev's resignation still needs to be approved by parliament on 20 February.
(with material from AFP)