But government representatives will remain in Kuwait where they will continue to take part in indirect talks through UN mediator Ismail Ould Cheikh Ahmed, delegates said.
"We have decided to suspend direct talks with the rebels to protest continuing violations of the ceasefire" that came into effect on April 11, a senior government official told AFP.
"We call on the United Nations to act seriously to end these violations which threaten to undermine the peace talks," said the government official who declined to be named.
Yesterday, Yemen's warring parties held their first face-to-face talks since the negotiations opened in Kuwait on April 21.
The UN envoy said these direct talks were "productive" and had touched on key issues.
But later yesterday, the rebels and their allies overran Al-Amaliqa base in northern Yemen after hours of clashes, tribal and military sources said, adding that the fighting caused casualties.
The sources said that the commanders of the 600-strong brigade, located in the rebel stronghold province of Amran since 2014, had "chosen to remain neutral" as pro-government forces, backed a Saudi-led coalition, clashed with the insurgents across Yemen.
Mikhlafi said his delegation will take "a suitable position" towards the rebels' "crime" against Al-Amaliqa base without elaborating.
Yemen's warring parties have repeatedly traded blame for ceasefire violations.
Government loyalists said they have recorded "3,694 ceasefire violations by the Huthis and their allies" -- troops fighting in support of former president Ali Abdullah Saleh.
Meanwhile, the rebels accused government forces and the Saudi-led coalition backing them of 4,000 breaches.
The coalition in March 2015 launched a military campaign against the rebels, who have seized the capital Sanaa among other parts of the country.
Rebel spokesman Mohammed Abdulsalam wrote on Facebook yesterday that Saudi Arabia freed 40 Yemeni rebel prisoners, as part of a deal reached with the kingdom in March to calm the situation along the border.
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