The US military is investigating air strikes it carried out this month in Afghanistan which Kabul said killed 17 "insurgents" but local officials and witnesses insisted Thursday were civilians.

US forces regularly launch air strikes in the name of counter-terror operations in the eastern regions bordering Pakistan, where the Taliban, Islamic State group and Al-Qaeda fighters have strongholds.

On April 6 "US forces conducted two counter-terrorism strikes in Paktika" province, Brigadier General Charles Cleveland said in a statement to AFP.

"Currently there is no evidence of civilian casualties. However, we are conducting a thorough investigation into the strikes," he added, without saying why they were carried out or the number of victims.

Haji Hussain Khan, a tribal elder from Gomal district, said three drone strikes killed 17 people.

"They were civilians who were carrying weapons for their own protection as the area is not under government control," he said.

District governor Shaista Khan corroborated the account, saying those killed were members of the Kakarzai tribe returning from a meeting over a land dispute.

"The 17 victims were all civilians. There were youths and tribal elders among them," he said.

But an Afghan official, speaking on condition of anonymity, said the dead were "armed insurgents linked to Al-Qaeda".

"All the victims were armed insurgents," Paktika governor Aminullah Shariq added.

Later Thursday, Cleveland told Pentagon reporters in a video call that the US military conducted "just under" 100 counter-terrorism strikes in the first three months of the year in Afghanistan.

Most of these focused on the IS group and were carried out in Nangarhar province, on the border with Pakistan.

The strikes come at a fragile moment in Afghanistan, where local troops assumed responsibility for the country's security at the start of 2015, taking over from NATO forces.

Since then, the Taliban have hit local troops hard, including the brief capture of the major city of Kunduz, jolting confidence Afghan government forces can hold their own.

Cleveland said about 5,500 Afghan security forces were killed last year alone.

"That's very difficult for any military to sustain... but the military did not collapse," Cleveland noted, adding he was optimistic Afghan forces would fare better in 2016.

Further complicating the picture, the US military estimates between 1,000 and 3,000 IS fighters are now in Afghanistan.

"It's probably on the lower end of that," Cleveland said.

The IS fighters comprise disaffected Pakistani and Afghan Taliban, as well as Uzbek Islamists and locals.

Also present are 100-300 Al-Qaeda fighters, Cleveland said, and are rivals of the IS group.