Yemen's southern separatists said Saturday they have taken control of the southern port city of Aden, the seat of the internationally recognized government of President Abed Rabbo Mansour Hadi, following days of clashes with government loyalists.

The separatists also took over the house of Interior Minister Ahmed al-Mayssari after he was evacuated by coalition forces, government officials said.

The Saudi-led coalition late on Saturday threatened military action to halt the fighting and ordered the separatists to withdraw from government military camps they seized in the southern port city. Riyadh called for an emergency summit to restore order.

The fighting erupted on Wednesday when forces loyal to the Southern Transitional Council (STC) attempted to break into the presidential palace in Aden, leaving three dead and nine injured. Immediately after, Hani Ali Brik, deputy chairman of the STC called its people to "topple" the government of Hadi.

Read more: Southern separatist leader calls to overthrow Yemen's government, three dead

The separatists and the internationally recognized government are nominally united in their battle against the Houthis. But they have rival agendas for Yemen's future.

The Saudi-backed government earlier called the move by the STC, which is backed by coalition member the United Arab Emirates, a coup.

"We call on all components and military formations of the Transitional (STC) ... to immediately return to their positions and withdraw from the positions that have been seized," coalition spokesman Turki al-Malki said in a statement.

The STC agreed to the ceasefire. "The spokesman of the Southern Transitional Council confirmed its adherence to the ceasefire called for by the leadership of the Saudi-led coalition," the council said in a statement.

The coalition ordered an immediate ceasefire as of 1:00 a.m. local time on Sunday, he said, and would use military force against those who violate it.

The violence complicates the United Nations' efforts to end a four-year war that has killed tens of thousands and pushed the poorest Arabian Peninsula nation to the brink of famine.

Four days of clashes between the separatists and government forces have killed at least nine civilians and more than 20 combatants, medical sources said. The fighting trapped civilians in their homes with dwindling water supplies.

An STC official told Reuters the separatists were in talks to peacefully take over the all-but-empty presidential palace in the predominantly residential Crater district, after it had been seized.

The separatists have moved into the interior minister's house after he was evacuated by coalition forces, officials said. President Hadi is based in the Saudi capital Riyadh.

Saudi Arabia's Vice Minister of Defense Khalid bin Salman called on parties in Aden to let prudence and dialogue prevail and unify ranks against the Houthis.

"We reject any use of arms in Aden and disturbing the security and stability, and we call for restraint…Therefore, the Kingdom called for a political dialogue with the legitimate Yemeni government in Jeddah," he said in a tweet.

The UAE, which has armed and trained thousands of southern separatist fighters, earlier called for calm and unity. Its foreign minister urged UN envoy Martin Griffiths, who is trying to de-escalate tensions across Yemen, to help as well.

(With input from Reuters)