Before the motion was debated, Mr Kan told his party he would step down when the crises were under control. He was trying to head off a rebellion by senior members of his party which could have forced him from power.
March's disaster killed thousands of people and crippled the Fukushima Daiichi nuclear plant.
Mr Kan has secured himself a few more months in power, but he has been left a weakened figure by the rebellion in his party.
When Mr Kan came to office last June, he was Japan's fifth prime minister in five years. He has already survived several attempts by his opponents to force him to step down.
This time, senior figures in his Democratic Party of Japan (DPJ) had indicated they would support the no-confidence motion, increasing his chances of being forced out.
In a last-minute attempt to rally support, he urged a meeting of DPJ politicians to reject the no-confidence motion.
(BBC/VOVNews)
