Global charity Save the Children said it was suspending life-saving work in Aden as its staff were forced to hunker down amid gun battles that the Red Cross says have killed at least 36 people in the past three days.
A number of ministers fled the port city by boat on Monday night, docking in the district of Brega further west, a military source told AFP.
A port official confirmed their arrival, saying they were transported to a base of the Saudi-led coalition which backs Yemen's government.
But the ministers returned to Aden before dawn, after receiving guarantees from the coalition that the presidential palace would not be stormed, a government source said.
The source said Saudi Arabia and its coalition allies are now in talks with southern separatists and with Yemen's government, which Riyadh supports in the war against Iran-backed Huthi rebels.
The separatists, who advocate for self-rule in southern Yemen, now control seven of Aden's eight districts.
Forces loyal to the government of President Abedrabbo Mansour Hadi hold the large northern district of Dar Saad, while ministers remain in the besieged presidential palace near the coast.
Hadi's government has accused the separatists of attempting a coup in Aden, opening yet another front in the country's devastating conflict.
Save the Children
Save the Children on Tuesday said it was suspending critical humanitarian work in Aden out of fear for the safety of its staff.
"Our staff are forced to shelter at home and in bunkers while gun battles rage outside," Yemen Country Director Tamer Kirolos said, saying children are "dying every day from preventable causes" like hunger, cholera and diphtheria.
"Aden was a relative refuge amidst the fighting in Yemen, but now that too has been shattered," Kirolos said. "How many more innocent children must have their lives destroyed before the world takes notice?"
The southern port city of Aden has served as the government's base since 2014, when the Iran-backed Huthi rebels -- who hail from northern Yemen -- took control of the capital Sanaa.
Armed supporters of the separatist Southern Movement patrol a street following clashes in the southern port city of Aden, Yemen, 28 January 2018. Source: AAP
While President Hadi now resides in Riyadh, two military officials said Prime Minister Ahmed bin Dagher and a number of senior government figures remain in the Aden presidential palace.
For three years, Hadi's Saudi-backed administration was allied with the separatists, driving the Huthi rebels out of the south and back to their northern strongholds.
But tension between the allies began to surface in April when Hadi dismissed cabinet minister Hani bin Breik and Aden's governor in a move widely seen as reflecting divisions among his supporters.
Tensions boiled over into armed clashes between the separatists and pro-government forces on Sunday, fuelling chaos in the impoverished Arabian Peninsula country where a civil war has already left thousands dead and millions on the brink of starvation.
Demand for self-rule
Under the self-proclaimed Southern Transitional Council (STC), the separatists have gained traction since April in their push for self-rule, demanding the reinstatement of South Yemen as an independent entity.
The STC this month called on Hadi to make changes in his government, accusing him of corruption and mismanagement.
The clashes have sparked fears of a repeat of the 1986 South Yemen civil war, a failed socialist coup which killed thousands in just six days and helped pave the way for the 1991 unification of South and North Yemen.
Fighters loyal to the separatist so-called Southern Transitional Council, backed by the United Arab Emirates, near the presidential palace, in Aden (AAP) Source: AAP
Brigadier Saleh al-Sayyed, who heads troops that have fought alongside the separatists since Sunday, announced his forces had seized control of the Fourth Brigade, the presidential guard in Aden.
Yemen's president has urged Saudi Arabia and its allies to intervene to defend the government.
The coalition said it would take "all necessary steps to restore security" but has not announced any new operation to help the government in Aden.
The United Arab Emirates, a key coalition member that has trained up a special operations force in the Yemeni army, has close ties to sacked minister bin Breik, a prominent separatist.
The UAE-trained force, dubbed the "security belt", is stationed in southern Yemen and supports the STC. Some troops in the Yemeni army are also loyal to the separatists.
The coalition on Monday called on the separatists to exercise restraint, while urging the Yemeni government to "take into consideration the demands of the social and political movement" in the south.
