The ministers submitted their resignation to Prime Minister Baburam Bhattarai at the secretariat of the Special Committee where the agreement was discussed and signed, the Republica.com reported.
Deputy Prime Minister and Minister for Foreign Affairs Narayan Kaji Shrestha announced the resignation of all the Maoist ministers while Minister for Physical Planning made the similar announcement on behalf of the ministers representing the United Democratic Madhesi Front (UDMF).
Bhattarai will form a new coalition government including members of the main opposition parties, officials said.
No date for the formation of the new government was announced. Nepal's parliament has, until May 27, to write a new constitution, which will divide the country into new states.
The assembly was elected in 2008 with a mandate to draft the document within two years, but the deadline has been repeatedly extended amid little progress.