CAIRO — A Saudi-led military coalition fighting in Yemen targeted its own allies with airstrikes Sunday, a day after southern separatists seized control of the strategic port city of Aden, threatening to fracture the Saudi alliance and open a new front in the five-year conflict.

Even before the damage from those strikes had been assessed, the United Nations on Sunday said that as many as 40 people have been killed and 260 injured in the previous four days of clashes in Aden that erupted on the eve of one of Islam’s holiest periods, Eid al-Adha. Tens of thousands of civilians in the Red Sea city nestled on the tip of the Arabian Peninsula have fled their homes, while many others remain trapped without basic necessities, U.N. officials and aid workers said.

“It is heartbreaking that during Eid al-Adha families are mourning the death of their loved ones instead of celebrating together in peace,” Lise Grande, the top U.N. humanitarian official Yemen, said in a statement. “Our main concern right now is to dispatch medical teams to rescue the injured. We are also very worried by reports that civilians trapped in their homes are running out of food and water.”

Yemen, the Middle East’s poorest nation, was already in the grips of what the United Nations has described as the world’s worst humanitarian crisis.

The seizure of Aden has exposed divisions within a Sunni Muslim coalition led by Saudi Arabia and the United Arab Emirates that intervened in the conflict in March 2015. Together, they have been battling Iran-allied, Shiite rebels known as Houthis to restore Yemen’s internationally recognized government and prevent Tehran from gaining regional influence.

“This weakens the coalition by exposing undeniable cracks beneath the surface,” said Elisabeth Kendall, a Yemen scholar at Oxford University’s Pembroke College. “It is becoming increasingly obvious that the UAE and Saudi Arabia do not share the same end goals in Yemen, even though they share the same overarching goal of pushing back the perceived influence of Iran.”

Rifts have emerged over the past 18 months between the southern separatists, backed by the UAE, and forces aligned with Yemen’s government, backed by Saudi Arabia. 

The separatists, who want to split Yemen’s south from its north, have long been suspicious of the Yemeni government, ruled for decades by northerners. The separatists, and the UAE, also disapprove of Yemeni President Abed Rabbo Mansour Hadi’s alliance with Islah, an influential Islamist party. While the Saudis consider Islah vital for rebuilding Yemen, the UAE is opposed to any significant role for Islah because of its ties to the Muslim Brotherhood, a regional political Islamist movement that the Emirati leadership views as a domestic threat, as well as a malign and radical force in the Arab world.

Clashes engulfed Aden’s streets after a missile attack on a military parade killed dozens of separatists fighters and a prominent commander last week. The Houthis claimed responsibility for the strike, but the separatists accused Islah of playing a part.

The violence was a major blow to Saudi Arabia and its ambition of restoring Yemen’s government. Aden had served as the government’s headquarters for several years, while Sanaa, Yemen’s capital, has been under the control of the Houthis since they forced the government from power.

Statements from Saudi officials framed the violence as a worrying distraction from the campaign against the Houthis.

The Saudi foreign ministry said it had invited the Yemeni government and “all parties involved in the conflict in Aden to hold an urgent meeting in Saudi Arabia to discuss disputes, give priority to prudence and dialogue, and unify ranks.” Col. Turki al-Malki, a spokesman for the Saudi-led coalition, called for a cease-fire to begin early Sunday and for “all parties to withdraw from positions they have seized.”

Prince Khalid bin Salman, the vice minister of defense and a brother of Saudi Arabia’s de factor ruler, Crown Prince Mohammed bin Salman, wrote on Twitter that “violence in Aden will create a situation that could be utilized by terrorist organizations like the Houthis, al-Qaeda/ISIS, which KSA will never condone.”

Al-Qaeda and the Islamic State appear to be taking advantage of the security vacuum in Yemen’s south, said Kendall, who monitors both groups. In the first week of August, al-Qaeda undertook seven operations in as many days targeting UAE-backed forces, a significant uptick in attacks. And the Islamic State launched two attacks in Aden, the first time it has targeted the city in more than a year.

Despite the calls for a cease-fire, the Saudi-led coalition opted to send a warning to the separatists with airstrikes late Saturday and early Sunday. The coalition did not specify where the attacks occurred, but separatist officials and aid workers said areas in the Dar Saad and Khormaksar districts, as well as around the presidential palace, were hit.

“This is only the first operation and will be followed by others . . . the Southern Transitional Council still has a chance to withdraw,” Saudi state TV quoted the coalition as saying, according to Reuters.

On Sunday, though aid agencies and residents reported that fighting had subsided, there were no signs that separatists were leaving the positions they had seized.

Yemen’s information minister, Moammar Al Iryani, called the seizure of Aden a “coup against constitutional legitimacy” and likened it to the Houthi takeover of Sanaa.

Nizar Haytham, a spokesman for the Southern Transitional Council, said “no coup has taken place.” The separatists, he added, had a right to secure southern Yemen from “northerners who possess absolute hostility toward the south.” He then described the Islamists in the Hadi government as “al-Qaeda members” with “military titles.”

In a video shared on social media Sunday, a top separatist leader, Hani Bin Brek, said they were willing to negotiate with the coalition and the Hadi government, but “not under threats.” He warned the Saudis to not continue their airstrikes.

Caroline Seguin, the Yemen program manager for Doctors Without Borders, said the organization’s hospital in the city had been overwhelmed with patients. “It has been a big nightmare,” she said, noting that the hospital received 120 injured patients in a 24-hour period. 

The majority of the casualties were civilians injured by explosions. Six people, including a child, were dead by the time they arrived at the hospital, she said. Yemeni health officials she spoke to Saturday said all the city’s hospitals and some of its private clinics were also full of patients wounded in the fighting. 

With the airport closed, the group, also known by its French acronym, MSF, was trying to bring reserve medical supplies to the hospital from Djibouti by boat, Seguin said.

Last year, after clashes erupted in Aden, Saudi Arabia and the UAE brokered a truce between both sides, leading to an uneasy alliance. Most analysts said they expect further clashes, because the grievances between the two sides have only deepened.

“At the leadership level, the coalition will likely paper over the cracks and continue to work together,” Kendall said. “But at ground level, trust has been lost and it will be increasingly difficult to integrate southern forces into the Hadi-controlled Yemeni military.”

The north-south tensions also raise questions about a fragile U.N.-brokered cease-fire agreement in the western port city of Hodeidah, north of Aden. U.N. officials view it as a key step toward a peace deal to end the war. But “the recent clashes show that a broader, more inclusive, and hence more complex, approach is needed,” Kendall said.

Fahim reported from Istanbul and Al-Mujahed reported from New Delhi.