They have conducted a series of suicide attacks in Sanaa since early this year that killed more than 100 people.
The blast happened in the Balili mosque near a police academy in Sanaa, which is controlled by the Huthi insurgents, according to witnesses, a few of whom reported dead and wounded.
“We strongly condemn the suicide bomb attack on Sanaa’s Belili Mosque, which was carried out during Eid-al Adha prayers and which claimed numerous lives”, the ministry declared in a statement.
The attack comes two days after Yemen’s President Abdrabbuh Mansour Hadi returned to the city of Aden from exile in Saudi Arabia.
On September 13 forces loyal to Hadi, backed by the Saudi-led coalition, launched a major ground offensive against rebels in the province of Marib, east of the capital.
The Islamic State in Iraq and the Levant (ISIL) claimed responsibility for the attack, which also left dozens of people injured.
Hadi’s office said the government would not attend talks unless the rebels first accept UN Security Council resolution 2216 demanding their withdrawal from territory they have captured.
However the Houthis – Shia Muslim rebels from the north of the country – still control the capital.
The internationally recognized leader of Yemen, Hadi arrived in Aden aboard a Saudi military aircraft that landed at an airbase adjoining the civilian airport in the southern port city.
Hundreds of others were wounded and many public and private properties destroyed in the air raids, it said.
A security vacuum in Aden and much of Yemen’s south, which were won back from the Houthis in July, may yet delay the regrouping of the Yemeni state there as armed gangs and al Qaeda militants have stepped up their presence.
Saudi-owned al-Arabiya television said on Thursday at least 40 Houthis were killed while trying to sneak into a Saudi village across the border with Yemen.
It has distanced itself from Daesh’s tactics, saying that it avoids targeting mosques to protect “innocent Muslims”.