Abdulmalek al-Mikhlafi said on Twitter that the Huthi Shiite militia which controls the capital had "torpedoed the talks completely," by backtracking on their commitments after a month of negotiations.
"I have asked the UN envoy not to allow the rebels to waste any more time... And to make them comply with the reference issues before we resume the talks," said Mikhlafi, who heads the government delegation.
A statement by the government delegation said it would continue to boycott the talks until the rebels comply with the agreed references.
The statement blamed the Huthis of destroying the country's economy, refusing to respect the ceasefire and to implement UN Security Council resolutions.
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In particular the government wants the Huthis to comply with a UN Security Council resolution ordering them to pull out of territory they occupied in a 2014 offensive and surrender heavy arms they captured.
Sources close to the government and rebel delegations confirmed to AFP that a session scheduled to take place this morning was cancelled after the government delegation withdrew.
The two delegations were on the verge of finalising a deal to release half of the detainees and prisoners before the start of the Muslim holy fasting month of Ramadan in early June.
The United Nations estimates that more than 6,400 people have been killed and 2.8 million displaced in Yemen since March last year.
A major stumbling block at the talks in Kuwait City remains the form of government that would control Yemen in a transitional period.