Mali has been left reeling from sweeping attacks by jihadists and separatist rebels who seized several towns and military bases and killed the defence minister and military intelligence chief.

The weekend assault on the west African state’s security architecture was coordinated by al-Qaida-affiliated Jama’at Nusrat al-Islam wal-Muslimin (JNIM) and the separatist Tuareg-led movement Azawad Liberation Front (FLA) – former foes with distinct agendas.

Mali’s defence minister, Sadio Camara, was killed in an attack on his residence in the garrison town of Kati, the country’s junta-run government said. A spokesperson said a car laden with explosives was driven by a suicide attacker into his residence and that in an ensuing firefight Camara sustained injuries from which he later died in a hospital.

The military intelligence chief Modibo Koné was reportedly also killed.

The attackers used car bombs and armed drones in their assaults on Kati – a junta stronghold just outside the capital, Bamako – as well as the eastern city of Gao and central towns of Mopti and Sévaré.

Heavy gunfire and explosions were heard near Modibo Keita international airport and the main military base at Kati. The airport was temporarily closed.

Videos emerged on social media of jihadists laughing and relaxing at the residence of the governor of Kidal, a town 250 miles (400km) south of the Algerian border. The Guardian has not independently verified the footage.

JNIM and FLA were among the lead actors in the ousting of Ibrahim Boubacar Keïta’s civilian government in 2020. Another coup in May 2021 led to Assimi Goïta, a young captain, becoming head of the junta and the denouncement of an existing peace deal between the government and the rebels.

Goïta, believed to be guarded by a private military outfit from Turkey, which has provided military support for Mali in recent years, is yet to comment publicly on the weekend’s attacks.

Authorities are yet to provide a death toll, but said on Sunday that the assault was over. Speaking on state TV on Sunday night, Gen Oumar Diarra, the chief of general staff, said the army had left Kidal but that Malian forces had “neutralised” more than 200 terrorists across the country and recovered ammunition.

The FLA spokesperson Mohamed El Maouloud Ramadan claimed soldiers from Africa Corps – the successor to Russia’s mercenary Wagner Group – had left Kidal, long coveted by the separatists as their capital, after an agreement was reached for their peaceful exit.

Mali has long battled militants linked to al-Qaida and Islamic State as well as a separatist rebellion in the north. Islamic State – Sahel Province (ISSP), formerly known as Islamic State in the Greater Sahara (IS-GS), was not heard from at the weekend.

Like other countries in the region that fell to juntas, Mali reached a security agreement with the Yevgeny Prigozhin-led Wagner Group after turning away from western allies for help in combating Islamic militants. Camara oversaw the transition to Africa Corps after the death of Prigozhin in August 2023.

The partnership failed to produce results. For months last year, JNIM enforced a blockade of fuel trucks from neighbouring Côte d’Ivoire and Senegal, cutting off crucial supply to the capital until a deal was reached.

Over the weekend, an Mi-8AMTSh helicopter belonging to Africa Corps was reportedly shot down by a surface-to-air missile near Gao, with everyone onboard killed.

According to Ulf Laessing, the Bamako-based head of the Sahel programme at the German thinktank the Konrad Adenauer Foundation, the attack was a serious setback for Moscow’s ambitions in the region. “For Russia the attack has been a disaster,” Laessing told Reuters. “They were unable to prevent the fall of the highly symbolic Tuareg stronghold of Kidal and now need to leave this northern city.”

Meanwhile, there have been reports of an Ivorian aircraft conducting surveillance at the border. Côte d’Ivoire – seen, like Nigeria, as a French puppet by the Malian junta – has been pursuing American collaboration in its north for cross-border operations into Mali and Burkina Faso, another jihadist-hit Sahelian country.

In the Nigerian capital, Abuja, the Economic Community of West African States (Ecowas) issued a statement on Sunday calling for “all states, security forces, regional mechanisms and populations of west Africa to unite and mobilise in a coordinated effort” against insurgency.

Mali split from Ecowas to form the parallel Alliance of Sahel States (AES) in 2025, alongside Burkina Faso and Niger. Ibrahim Traoré, Burkina Faso’s military ruler and AES chair, said the attacks in Mali were “backed by the enemies of the Sahel liberation struggle” but did not give any supporting evidence.

The UN secretary general, António Guterres, expressed deep concern over the violence, emphasising the vulnerability of an estimated 5 million people in Mali who were in need of humanitarian aid.