• Taliban routed after two months of fierce fighting, says Pakistan
• Aid agencies warn 1 million returning refugees still at risk

Two million people displaced by fighting in north-west Pakistan started returning home in military-protected convoys today, triggering warnings from international relief agencies that the reverse exodus was too fast and too soon.

Buses and trucks lined up outside crowded refugee camps to take the first batch of refugees back to their homes in the Swat valley, where the army says it has routed the Taliban after two months of sporadic combat.

Pakistan’s government is keen to reverse the mass migration, which is comparable to that triggered by the Rwandan genocide of 1994, because it has left limited resources severely strained.

At least 1 million people have been displaced from the main battle zone in the valley, with another million or so fleeing neighbouring Dir and Buner. About 300,000 are living in camps; the rest are sheltering with friends or family.

The government is providing the refugees with convoys of buses, military protection and cash payments to help them resettle. Officials say the process will take two weeks.

But some aid workers say the process has been poorly conceived and people are vulnerable to further attack.

“The Pakistani government is sending people home far too early,” said Kristèle Younès, of Refugees International. “Displaced people should be the ones to determine whether it is safe for them to return, and we fear the government is not providing them with clear and accurate information.”

“There are some suspicions that [the return] is not as free as you would like,” said Dorothy Blane of Concern. “They should not be forced back just so the government can say that normal life has returned, because if they have to come out again it will be a disaster.”

The return process got off to a slow and chaotic start. Residents trying to travel to Swat in private cars were turned back at the town of Sher Gur, on the edge of the conflict-affected area.

However, buses carrying people from Jalozai, an old Afghan refugee camp in Nowshera, were allowed through. Army helicopters circled overhead, offering protection from any attack.

Amir Haider Khan Hoti, the chief minister of North West Frontier province, told one group the Taliban would soon be finished. “I assure you that in this war of survival for Pakistan, we – and you – will win,” he said.

The Pakistani army claims to have killed more than 1,700 Taliban fighters in Swat and the neighbouring districts of Buner and Swat. The figure cannot be confirmed. The Taliban have been cleared from the main areas of Swat, including the main city, Mingora, which is believed to have suffered far less damage than had been feared.

But the army has failed to kill the Taliban leadership, igniting concerns that the militants could re-emerge under the cover of the civilian population. Last week the army said the Taliban leader, Maulana Fazlullah, had been badly injured.

In a reminder of how the militant threat is spreading, an explosion at a madrasa religious school in central Punjab province killed 13 people today. The cause was unclear but appeared to be an explosives cache.

Many refugees are also concerned that the government has made inadequate preparations for a return to normal life, according to Muhammad Niyaz, of Islamic Relief. “Crops have been destroyed and businesses damaged [during the fighting]. The majority say they will not go back until they are sure there is something for them on the ground,” he said.

To counter the threat of a Taliban resurgence the authorities are raising a local civilian militia, known as “community police”, to help flush out Taliban infiltrators.