The ministers said in a statement: "We have decided to leave our posts after we have seen the mismanagement of the prime minister. He sacked the mayor of Mogadishu without consulting the council of ministers."
Among those who signed the statement are the foreign and defence ministers.
The ministers said that they would continue to serve in office until Nur could replace them.
"No initiatives were launched in parliament for the last seven months and there was a total misuse of the nation's resources, while the government also failed to ensure security," they said in their statement.
|Aid workers have withdrawn from Somalia because of worsening security [EPA]
Mohammed Adow, Al Jazeera's correspondent, speaking from the Kenyan capital Nairobi, said the resignations were a huge blow to the government of Yusuf, because it showed that there were so many political problems in Somalia, on top of the raging insecurity, the humanitarian problems and the hunger crisis.
"The prime minister is the leader of the executive arm of the government and the president is the head of state, but there has always been a problem with the Somali constitution, and who has the most power," he said.
The fresh crisis in war-torn Somalia comes amid efforts by international and Somali brokers to press on with a peace process aimed at ending the civil fighting that has killed thousands in recent months.
Ethiopian troops came to the rescue of Somalia's embattled and internationally backed transitional government in late 2006, forcing out the Islamic Courts' Union, the that had briefly controlled large parts of the country.
The group and remnants of the group have since waged a deadly guerrilla war against government targets, Ethiopian forces and African Union peacekeepers.
International rights groups and aid agencies have said that at least 6,000 people were killed and hundreds of thousands displaced over the past year alone, with civilians bearing the brunt of the fighting.
The UN sponsored a new peace initiative which led to the signing on June 9 in Djibouti of a truce agreement between the government and the main opposition movement.
But the deal led to a split in the opposition, with conservative Muslim groups insisting that Ethiopian troops should leave before negotiations start.
The build-up to the truce agreement - which has yet to have any substantial impact on the ground - also sparked tensions between the Yusuf and Nur, officials have said.
Ahmedou Ould-Abdallah, the UN special envoy for Somalia, has expressed concern at the political situation and urged all parties to work together.