Among those resigned are four Cabinet, four state & one deputy minister.
The ministers will however remain part of government MPs and sit in the parliament as backbenchers.
The group called for an end to communal politics and urged to expedite investigations into Muslim leaders standing accused in the aftermath of the Easter Sunday bombings.
Leader of Sri Lanka Muslim Congress (SLMC) and Minister Rauf Hakeem said innocent Muslims are at the receiving end and many of the Muslims now in police custody over suspected links to terrorism are innocent.
Earlier in the day, two provincial governors resigned amidst protest in various parts of the country demanding their resignations.
Eastern Province Governor M L A M Hizbullah said in his resignation letter that there has been a calculated attempt to discredit the Muslim community and create fear psychosis after Easter Sunday attacks.
The governor said he has been made to understand that Muslim community safety cannot be guaranteed unless he resigns. Meanwhile, a Buddhist monk who is also a MP ended his hunger strike after the resignations.
The monk launched the strike demanding the removal of a Muslim minister and the two governors.
Thousands of people marched on the streets in Kandy where the monk undertook hunger strike, to support his cause. Similar protests were organized in other parts of the country.
Buddhist monks accuse the three leaders of supporting the terrorists responsible for the Easter attacks that killed 258 people including 45 foreigners.