Southern separatists in Yemen called on supporters to overthrow the Saudi-backed internationally-recognized government of President Abd-Rabbu Mansour Hadi and clashed on Wednesday with presidential guards in Aden, leaving three dead and nine injured.

Aden is the temporary capital of Yemen's internationally recognized government, and home to Hadi, though he himself is in Saudi Arabia and the presidential palace is largely empty apart from soldiers.

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, and a missile strike in Aden last week that killed dozens of southern soldiers raised friction between them. Separatist commander Brigadier General Muneer al-Yafee was among those who died in the missile attack. 

Just before Wednesday's clash, hundreds of separatist supporters attended a funeral for some of the southern soldiers and a prominent commander near the hilltop presidential palace. As the crowd chanted anti-government slogans, shooting was exchanged with presidential guards.

Presidential guard Brigadier General Sanad al-Rahwa confirmed his forces had clashed with the separatists, arguing the armed groups tried to storm the presidential palace and central bank. Hani Ali Brik, deputy chairman of the Southern Transitional Council, said their people just wanted a peaceful sit-in in front of Al-Yamamah palace, but were targeted by live fire from Islah's militias, a Yemeni Islamist party who has a close relation with Saudi Arabia since the civil war in Yemen. The south separatists accused the Islamist party Islah, an important ally of Hadi,  to have been complicit in last week's missile attack.

After the funeral, Ali Brik called on supporters to march toward the Maasheeq Palace in the southern coastal city to overthrow the government of Hadi.

"We announce a general mobilization of all our southern forces to march toward the Maasheeq Palace," Ali Brik said, but there was no sign such a march had begun.

Interior Minister Ahmed al-Mayssari said the government had so far practiced restraint to maintain stability in Aden but was "fully ready" to combat any actions targeting the state's institutions.

"We call on the Yemeni people not to respond to such calls as they only aim for war and only serve the Houthis," he said.

The United Nations' special envoy for Yemen, Martin Griffiths, expressed concern about the flare-up in Aden.

"I am alarmed by the military escalations in Aden today, including reports of clashes in the vicinity of the Presidential Palace. I am also deeply concerned by the recent rhetoric encouraging violence against Yemeni institutions," he tweeted.

A senior United Arab Emirates (UAE) official, Anwar Gargash, called for calm after the violence, which he described on Twitter as worrying. He said escalation between the two sides was not acceptable after attacks claimed by the ISIL and Al-Qaeda in southern Yemen in recent days. The UAE supports the anti-Houthi coalition but also backs the southern separatists. 

The Saudi ambassador to Yemen said the only beneficiary of the violence was the Houthis.

(With input from Reuters)