Bamako: Malian troops searched house-to-house in Timbuktu on Monday morning following hours of fighting with Islamist rebels who had infiltrated the northern desert town.

Residents said calm had returned by late Sunday after heavy clashes and airstrikes by French fighter jets backing the Malian troops forced them to shelter indoors.

The fighting reflected the difficulty of securing Mali after a French intervention in January that pushed the rebels out of their northern strongholds.

“Things are quiet this morning. The markets are open, traffic is on the streets, and people are out of their houses,” Timbuktu resident Garba Maiga said by telephone.

Malian military sources said soldiers were sweeping parts of the town to ensure there were no remaining rebel fighters.

At least one Malian soldier was killed in the clashes, along with more than 20 insurgents, according to a government statement on Sunday night. Residents said at least five civilians were killed in the crossfire.

An army spokesman said that groups of rebels had entered the town after setting off a suicide car bomb at a checkpoint, diverting the military’s attention.

Paris is keen to reduce its current 4,000-strong troop presence to 1,000 by the end of the year as it hands over its mission to a regional African force.

“For the moment it’s calm in Timbuktu. We have the situation under control,” a Malian officer said.

“Our team on the ground is sweeping (the city) and checking whether any jihadists are still active or not.”

A resident confirmed the fighting had died down.

“There are no more gunshots, but everyone is staying home,” he said.

The Islamists began their assault late Saturday with a suicide bombing at an army checkpoint on the edge of Timbuktu that wounded a Malian soldier.

Militants then infiltrated the fabled Saharan city, which French and Malian soldiers recaptured from Islamist rebels in January after a 10-month occupation.

They opened fire on two sides of the city centre, targeting a Malian military base and a hotel serving as a temporary residence for the governor.

France sent in a unit of around 50 soldiers to help the Malian army and dispatched fighter jets to back them up.

Three Islamists and one Malian soldier were killed in the fighting, officials said.

A French soldier was wounded, the military said in Paris. Four Malian soldiers were also wounded, officials there said.

An army source requesting anonymity said a Nigerian civilian who had been taken hostage also died during a shoot-out between Malian troops and his captor - an Islamist rebel seen wearing a bomb-belt who had holed up in a house in the northern part of the city.

It was unclear whether the pair had been killed in the firefight or the hostage-taker had detonated his belt.

A Malian security source said occupants had been evacuated from the targeted hotel, including the regional governor and two foreign journalists.

Mali has been the target of a series of attacks claimed by Islamist insurgents since France launched a military operation in January against Al-Qaida-linked groups occupying the north of the country.

The French-led operation has forced the extremists from the cities they seized in the chaotic aftermath of a military coup that overthrew Mali’s government in March 2012.

But French and African forces have faced continuing suicide blasts and guerrilla attacks in reclaimed territory.

On March 21, a suicide bomber blew up a car near the Timbuktu airport at the start of an overnight assault on the city.

One Malian soldier died in the blast. Around 10 Islamist fighters were killed in the ensuing fighting with French and Malian forces.

That assault was claimed by the Movement for Oneness and Jihad in West Africa (MUJAO), one of three Islamist groups that had seized the north.

MUJAO said it had “opened a new front in Timbuktu”, which had not come under attack since French-led forces entered the city on January 28.

No group has so far claimed last weekend’s attack.