"I am happy to say that following intensive efforts... We have reached a ceasefire" between the sides fighting in Saada province, Jamal Benomar told reporters.
A Red Cross convoy entered the village of Dammaj, where the Islamists are besieged by the Huthis, and the International Committee of the Red Cross said its teams had evacuated 23 critically wounded people.
"There are still more wounded people in need of treatment, and we hope to be able to come back for them," the ICRC director in Yemen, Cedric Schweizer, said in a statement.
"I hope this ceasefire will be permanent, and I hope that efforts will follow to find a solution for the roots of this problem," Benomar said, while also warning the conflict "threatens the security of Yemen".
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"Large groups of gunmen are being mobilised from different areas. This would have serious security implications," he added.
Dammaj, where a school for Sunni preachers has operated since the 1980s, has been the scene of frequent clashes between Sunni Islamists and the Huthis, for whom Saada is a stronghold.
The fighting with mortar and rocket fire concentrated on the Mazraa mosque and a Koranic school held by the Islamists in Dammaj and surrounded by rebels.
On Saturday, the defence ministry's news website reported a ceasefire and said troops had been deployed in areas evacuated by the rival sides.
A statement by the Huthi rebels accused Sunni extremists of having "transformed the centre of Dammaj into a real barracks for thousands of armed foreigners".
The Huthis, who are members of the Zaidi Shiite community, rose up in 2004 against ex-president Ali Abdullah Saleh's government, accusing it of marginalising them politically and economically.