Yemen’s government accused the United Arab Emirates of supporting separatists in the country and is demanding its expulsion from a Saudi Arabia-led coalition fighting rebels there, in a setback to U.S.-backed efforts to mend fraying ties within the alliance.

The U.A.E. joined the coalition in early 2015 on the side of Yemeni President Abed Rabbo Mansour Hadi’s government, after the Iran-aligned Houthi rebels captured the capital San’a.

Rival agendas for Yemen have since resulted in a widening rift in the Saudi alliance, threatening attempts to end a war that has caused a major humanitarian crisis. The conflict has become a flashpoint in the region amid heightened tensions between Iran and the U.S., which backs the Saudi coalition.

The Hadi government’s call to remove the U.A.E. comes after an Emirati-backed Yemeni faction within the coalition seized control this month of the southern port city of Aden, the temporary seat of Mr. Hadi’s government. The faction, called the Southern Transitional Council, is funded and trained by Emirati forces and fights alongside the Yemeni government against the Houthis.

But the separatist group has a rival goal of restoring an independent state in southern Yemen. It captured another two military bases in the southern city of Abyan, east of Aden, this week.