Pakistan Law Minister Zahid Hamid submitted his resignation to Prime Minister Shahid Khaqan Abbasi late on Sunday, media reports said.
There had been massive protests against Hamid in the capital Islamabad.
Hamid said he hoped his resignation would bring the crisis to an end.
"In order to restore peace, I have made up my mind to step down," media reports quoted him as saying.
The protesters had accused Hamid of blasphemy after rules that required lawmakers to reference the
Prophet Mohammed while taking their oaths were weakened.
The government had apologised, blaming the changes on clerical mistakes.
Hamid too had earlier apologised to the protesters.
Hamid, media reports said, was concerned about his safety after his ancestral home in Pasrur was attacked by protesters on Saturday.
The reports added that he wants the Pakistan Muslim League-Nawaz (PML-N) leadership to make certain his name is cleared of the controversy after his resignation.