Ar-Namys and Ata-Meken, two parties in the ruling parliamentary coalition, left the bloc this week, leaving the ruling coalition short of the majority needed to lead the 120-member Parliament.
Kyrgyz President Almazbek Atambayev signed a decree Friday dismantling the government, reports Russian news agency RIA Novosti.
Kyrgyz law stipulates the prime minister must resign and a new government must be formed if the ruling majority collapses.
A spokesman for the prime minister's office this week said early calls by members of the coalition for a new government were out of step with national laws in the former Soviet republic.
A 2010 coup toppled the government of President Kurmanbek Bakiyev. Atambayev, a former prime minister, secured the presidency by winning 63 percent of the vote in a subsequent election.
Hundreds of ethnic Uzbeks and Kyrgyzs were killed in ethnic violence after the coup. Human rights group say Bishkek has substantial work ahead to repair national divisions.
Duggar sisters unveil Christian dating rules in new book
McPhee, Cokas 'working on their marriage' after affair