The United Arab Emirates has said it will withdraw its remaining forces from Yemen, after Saudi Arabia backed a demand from the Yemeni presidential council for them to leave within 24 hours.

The Emirati announcement followed an air strike by a Saudi-led military coalition on what it said was a weapons shipment for UAE-backed separatist forces in the southern port of Mukalla.

The UAE denied the shipment contained weapons and expressed “deep regret” at the Saudi accusations.

Saudi and the UAE have been allies in the war against Yemen’s Iran-backed Houthi movement over the past decade, but the infighting between the rival factions they support has deepened a rift between them.

Saudi Arabia also accused the UAE of “pressuring” the separatists to attack Saudi-backed government forces in two eastern provinces, and warned it would take measures to confront such “highly dangerous” actions.

On Tuesday afternoon, the UAE’s defence ministry put out a statement announcing “the termination of the remaining counterterrorism personnel in Yemen of its own volition”, six years after the UAE’s armed forces had “concluded” their presence.

The ministry explained that the decision to withdraw them was made “in light of recent developments and their potential implications for the safety and effectiveness of counterterrorism missions”, without mentioning the coalition strike or Saudi warning.

The strongly worded statement issued by Saudi Arabia’s foreign ministry on Tuesday morning said it was working to “contain the escalatory steps” taken recently by the Southern Transitional Council (STC), which seeks independence for southern Yemen.

It accused the UAE of “pressuring” the STC to conduct offensives in the eastern provinces of Hadramawt and al-Mahra, which it said constituted “a threat to the kingdom’s national security, and the security and stability of the Republic of Yemen and the region”. It also warned that Saudi Arabia would take measures to confront such “highly dangerous” actions.

The UAE’s foreign ministry denounced the allegations that it “exerted pressure on, or issued directives to, any Yemeni party to undertake military operations that would undermine the security of the Kingdom of Saudi Arabia or target its borders”.

It also insisted that the UAE had “focused on containing the situation, supporting de-escalation efforts, and promoting understandings to contribute to preserving security and stability” since the start of the STC’s offensives.

The head of Yemen’s eight-member presidential council – which includes STC representatives – earlier announced that he was cancelling a joint defence pact with the UAE and ordering its forces to leave within 24 hours “in the interest of safeguarding the security of all citizens, affirming commitment to Yemen’s unity, sovereignty, stability, and territorial integrity”.

Rashad al-Alimi also declared a state of emergency for a period of 90 days, which he said was necessary to confront the Houthis and what he described as “the internal strife led by mutinous military elements that received orders from the United Arab Emirates”.

The STC’s leaders said the ultimatum for the UAE’s withdrawal was unilateral and had no legal basis, and insisted the UAE would remain a “main partner” in the battle against the Houthis.

Alimi’s announcement came after the spokesman of the Saudi-led coalition – which includes the UAE – said it had carried out a “limited” air strike on weapons and military vehicles for the STC’s forces in the southern Yemeni port of Mukalla which arrived on two ships from the UAE.

The shipments had constituted “an imminent threat and an escalation that threatens peace and stability”, Maj-Gen Turki al-Maliki asserted.

An official at the port told AFP news agency that a warning to evacuate was received at 04:00 local time (01:00 GMT) and that an open area at the facility was struck about 15 minutes later.

Pictures showed a number of burned out military vehicles and pick-up trucks in a walled-off area at the port, as well as damage to a nearby building. No casualties were reported.

The UAE’s foreign ministry said it had been surprised by the strike on Mukalla and that the coalition statement had been issued without consultation with member states.

It insisted that the shipment in question “did not include any weapons, and that the vehicles unloaded were not intended for any Yemeni party but were shipped for use by Emirati forces operating in Yemen”.

On Saturday, the Saudi-led coalition called on the STC’s forces to withdraw “peacefully” from Hadramawt and al-Mahra, a day after the Saudi air force reportedly bombed positions held by the separatists in the Wadi Nahab area of Hadramawt.

The STC’s forces launched offensives in the two provinces amid rising tensions earlier this month, putting them in direct conflict with government forces.

It said the operations were necessary to “restore stability” in the south and to combat the Houthis, as well as the jihadist groups al-Qaeda and Islamic State (IS).

Yemen has been devastated by a civil war that began in 2014, when the Houthis ousted the internationally recognised government from the capital Sanaa. The conflict escalated in 2015, after the Saudi-led coalition of Arab states intervened to restore the government’s rule.

The fighting has reportedly left more than 150,000 people dead and triggered one of the world’s worst humanitarian crises.

At the start of the war, the STC and other separatists seeking independence for south Yemen, which was a separate country before unification with the north in 1990, formed an uneasy alliance with the government to stop the Houthis capturing the southern city of Aden.

However, in recent years the STC and its allies have turned on the government and gradually seized control of Aden and much of the south of the country.