The first to go was the Minister of Minerals and Water Mohamud Salad Nur.
Three assistant ministers then announced their resignation less than a week after 18 senior officials also quit.
Eight more ministers and assistant ministers resigned after Prime Minister Ali Mohamed Gedi called for peace talks with rival Islamists to be postponed.
The talks had been scheduled for this week.
"We had no option but to resign because we believe if the talks are postponed again it will affect the reconciliation efforts," Minister of Fisheries and Ocean Resources Hassan Abshir Farah told Reuters.
"There are fears of war already. We swore to protect our people so that's why we thought we can no longer be part of this government."
The cabinet originally comprised 42 ministers, 11 of whom have resigned in the past week.
Government spokesman Abdirahman Dinari said the posts would likely be filled within a week.
Diplomats say power-sharing with the Islamists is the best way of averting a slide to war, deprived of effective central rule since warlords ousted dictator Mohamed Siad Barre in 1991.
The Islamists seized Mogadishu from US-backed warlords in June and now control much of southern Somalia, posing a challenge to the government's limited authority.
President Abdullahi Yusuf told residents in Baidoa, the government's provincial seat, they had a week to give up their weapons.
A cabinet colleague was shot dead there last week.
The news came as East African foreign ministers met in Kenya to discuss Somalia and how troops might be deployed there.
In what seemed like a rebuke to Ethiopia and Eritrea - who are both accused of backing the rival sides - east African body IGAD called on its seven members to not endanger peace.
"The Council called upon all member states to exercise restraint and ensure that their actions do not jeopardise the Somalia peace process," a joint communique said.
The United Sates has also called on foes Ethiopia and Eritrea to stay out of Somalia's escalating crisis.
Despite international pressure for negotiations between the two sides, talks stalled when the government accused the Islamists of breaking a pact against military expansion.
The Islamists have refused talks with the government, unless its ally Ethiopia withdraws troops from Somalia.
Further extending their influence in Somalia, the Islamists opened a new sharia court 600 km north of the capital today, local officials said.
"If the residents of every area in Somalia ask us to ... we should go and install Islamic courts," said Mohamed Qoryarey, leader of Islamic Courts' militia in the Adaado district of central Somalia.
The Islamist movement initially presented a moderate face, but the rise of hardline cleric Sheikh Hassan Dahir Aweys as its most influential leader has fuelled fears that the Islamists want to establish a Taliban-like state.