The heavily armed Huthis were in control of all three entrances to the Republican Palace, a building Prime Minister Khalid Bahah has lived in since taking office in October, a government spokesman told AFP.
The spokesman, Rajih Badi, called for an "urgent meeting" on Tuesday morning in order to create a "roadmap" to end violence, after a day of clashes between the Huthis and the army.
The Shiites appear to be tightening their grip on Sanaa after abducting an aide to President Abdrabuh Mansur Hadi, in the biggest challenge yet to his rule.
At least nine people were killed, including fighters from both sides, as the militia fired on Bahah's convoy, seized an army base near the presidential palace in Sanaa and took control of state media.
A ceasefire that came into effect after several hours appeared to be holding.
The Arab League, Britain and the United States expressed concerns about the clashes, which were the most intense in Sanaa since the Huthis overran it on September 21.
Since then strategically important Yemen has been wracked by unrest that has raised fears that Hadi's government will collapse and that the country will become a failed state similar to Somalia.
On Monday the Huthis claimed to have seized an army base on a hill overlooking the presidential palace.
Information Minister Nadia Sakkaf said they had also taken total control of state television and the official news agency.
STATE MEDIA OUTLETS SEIZED
"Yemeni satellite channel is not under state control, nor is state news agency Saba. The Huthis have completely controlled them and are refusing to publish any government statements," she tweeted.
This prompted head of the news department at Yemen state television Tawfiq al-Sharaabi to announce his resignation on Facebook.
Sakkaf said Huthis had also fired on Bahah's convoy as he left the presidential residence but that he was unharmed.
Witnesses said the fighting erupted early Monday after the militia deployed reinforcements near the presidential palace.
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The military presidential guard sent troops onto the streets surrounding the palace and outside Hadi's residence.
A security official said the army intervened when the Huthis began to set up a new checkpoint near the presidential palace.
But a prominent Huthi chief, Ali al-Imad, accused the presidential guard of provoking the clashes.
"Hadi's guard is trying to blow up the situation on the security front to create confusion on the political front," he said on Facebook.
Tensions have been running high in Sanaa since the Huthis abducted Hadi's chief of staff, Ahmed Awad bin Mubarak, in an apparent move to extract changes to a draft constitution that he is overseeing.
Mubarak is in charge of a "national dialogue" set up after veteran strongman Ali Abdullah Saleh was forced from power in February 2012 following a year of bloody Arab Spring-inspired protests.
The Huthis said they had seized him to prevent the violation of a UN-brokered agreement that provided for the formation of a new government and the appointment of Huthis as presidential advisers.
It stipulated that in return the Huthis would withdraw from key state institutions.
'SPIRALLING OUT OF CONTROL'
Mubarak's kidnapping came just before a meeting of the national dialogue secretariat to present a draft constitution dividing Yemen into a six-region federation, which the Huthis oppose.
The militants, who hail from Yemen's remote north and fought a decade-long war against the government, rejected the decentralisation plan last year, claiming it divides the country into rich and poor regions.
"The Huthis' decision to kidnap Mubarak was a serious escalation that now appears to be spiralling out of control," said April Longley Alley, an analyst with the International Crisis Group.
Since their takeover of the capital, the Huthis, also known as Ansarullah, have pressed their advance into areas south of Sanaa, where they have met deadly resistance from Sunnis including Al-Qaeda loyalists.
Yemen's branch of the jihadist network, Al-Qaeda in the Arabian Peninsula, is considered its most dangerous and claimed responsibility for this month's attack in Paris on French satirical weekly Charlie Hebdo that left 12 dead.
Hadi's government has been a key ally of the United States, allowing Washington to carry out regular drone attacks on Al-Qaeda militants in its territory.