French defence ministry confirms reports of Islamist deaths, together with at least 11 civilians including three children

Islamist militants are fleeing major towns in northern Mali after two days of air strikes by French troops, which sources say have left scores of rebels dead.

French fighter jets have pounded insurgent training camps, arms and oil depots as the French defence ministry confirmed reports of Islamist deaths, together with at least 11 civilians including three children.

"Mali is now at the mercy of the French army," said a well-connected Malian official in Bamako. "They are bombing the north, they have killed many terrorists. The Islamists have been running into the desert – they have deserted Gao and Timbuktu."

Residents in Gao confirmed French jets had struck the airport as well as the building that served as the base for the town's feared Islamic police. "The planes are so fast you can only hear their sound in the sky," Soumaila Maiga told Reuters. "We are happy, even though it is frightening. Soon we will be delivered."

Fighting has intensified in northern Mali since France made an unexpected decision on Friday to send troops into the country, to provide aerial support to Malian soldiers in the north, and protect its citizens in the south.

The former colonial power had previously said it would contribute training and logistical support to a planned African-led military intervention in September. But last week al-Qaida linked Islamists, who have controlled northern Mali since April, began advancing further south, prompting fears they could capture new ground.

Since the arrival of French Rafale fighter jets, which are reported to have dropped 250kg (550lb) bombs on militant targets, the Malian army has made significant gains, recapturing the towns of Konna and Douentza, just north of the de facto border between government-controlled southern Mali and the rebel-held north.

But there was uncertainty about the future plans for the French-assisted military operation. One analyst said there were concerns that Islamists were deliberately trying to draw the Mali army into the desert.

"My view is that al-Qaida in the Islamic Maghreb (Aqim) are trying to provoke the Malian army into making a general attack on the north," said Dr Jeremy Swift an expert on northern Mali. "The fighting would start at the beginning of the summer hot season, which is to Aqim's advantage; it starts before the Malian army have had much time to reorganise and train, and most important it starts before the international troop are fielded."

A diplomatic source in Bamako said France had considered the risks before deciding to intervene. "The French are being very careful, they are laying the ground properly; they are not pushing north too quickly," he said.

France's priority is to protect the military garrison in Sevaré, close to the strategic stronghold of Mopti, the last government-held city before Islamist control, the source said. "The point of the operation is not to rush north. This will be a continual attrition, while we wait for more forces to arrive here."

Mali state television announced the African troops, including up to 1,000 from Burkina Faso and Niger, were expected to begin arriving in the country on Sunday.

Britain has offered the use of its planes to transport troops; the US is providing support with communications and transport.

The UK sent the first of the RAF C-17 transport aircraft to France on Sunday afternoon, and the second is expected to leave RAF Brize Norton in Oxfordshire early on Monday. They will be packed with men and equipment and at least one of the aircraft should be in Mali on Monday.

The Ministry of Defence said no British combat troops were in Mali and none were expected to be sent. However, the UK has pledged support to a training mission in the country.

Before the crisis, military planners had thought of deploying two training advisers, who would probably not be in Mali before the end of this year. David Cameron will chair a meeting of the national security council on Tuesday to discuss the Mali crisis.

International efforts to support and train the Malian army were part of a repeatedly delayed plan for a west African regional military intervention in Mali, which last year won backing from the UN security council.

But a senior source in previous negotiations with the Ecowas west African bloc told the Guardian those plans were "in the bin" after France's intervention.

The French defence minister, Jean-Yves Le Drian, said France had more than 400 troops in Bamako, mainly to ensure the safety of French citizens and also to send a warning to the extremists.

Operation Serval as it is known – named after an African wildcat – is believed to have split French soldiers between Bamako and Mopti.

"We will strengthen our operation depending on the situation," he said on a political talk show with Itele and Europe 1 radio. Le Drian said Rafale jets will be part of the operation and technical support would be arriving in the next few hours.

Speaking on Friday, he said French intervention had prevented rebels driving south to seize Bamako, and air raids would continue. "The president is totally determined that we must eradicate these terrorists who threaten the security of Mali, our own country and Europe," Le Drian told French television.

Humanitarian groups expressed concern at the fighting and called on all parties in the conflict to respect civilians, amid concerns about casualties in the towns of Konna, Léré and Douentza.

"Because of the bombing and fighting, nobody dares to move in the city and the patients are unable to hospital," said Rosa Crestani, head of emergency programmes for Médecins Sans Frontières, which is providing treatment in Douentza.

"We are concerned for people living near combat zones and call on all parties to respect the fate of civilian populations and the integrity of medical facilities."

Human Rights Watch said about 10 civilians had been killed in the fighting, including three children who drowned trying to cross the river to safety.

"The resumption of active fighting brings grave risks for civilians," said its spokeswoman, Corinne Dufka. "Other children recruited by the Islamists in Gao have been wounded and possibly died in the fighting. The Islamists who have been recruiting kids from both Mali and Niger for months, must immediately release them.

"Furthermore, the Islamists' threats to retaliate against French non-combatants including hostages, are totally reprehensible and would constitute war crimes. All parties involved in this conflict – Islamist groups, Malian and French army, and Ecowas troops – should do all they can to protect civilians and strictly adhere to the law of war."