NATO forces in Afghanistan Tuesday admitted responsibility for the deaths of a civilian family of six in an airstrike in the southern province of Helmand last week.

The admission came a day after President Hamid Karzai summoned NATO's military commander and the US ambassador to warn that civilian deaths threatened the strategic pact he signed with US President Barack Obama last week.

"At this point in the investigation we are able to confirm the incident and will be formally apologising in the next couple of days to the family," a spokesman for NATO's International Security Assistance Force (ISAF) told AFP.

"We are deeply saddened by any civilian deaths, and particularly regret incidents where civilians are killed as a result of actions by ISAF," said Lieutenant Colonel Stewart Upton of ISAF's southwest regional command.

The Helmand provincial governor's office said in a statement that the family was killed unintentionally in an airstrike last Friday after ISAF checkpoints came under attack by insurgents in Sangin district.

"Unfortunately six members of the family including two boys, three girls and one woman were killed as a result of the incident," the statement said.

ISAF forces had apologised and promised to help the remaining members of the family, governor Mohammad Gulab Mangal said.

President Karzai told ISAF commander General John Allen and US ambassador Ryan Crocker that if Afghan lives were not protected the Strategic Partnership Agreement would "lose its meaning", a statement from his office said.

The pact covers relations between the two countries when US-led NATO forces helping Karzai's government fight a Taliban insurgency pull out in 2014.

Tens of civilians had been killed in NATO bombardments in four provinces in recent days, the statement charged.

Allen said after the meeting that he assumed personal responsibility for incidents in which civilians were killed and expressed condolences to the families involved, an ISAF spokesman said.

"He said he will fully investigate these incidents and report back to President Karzai," the spokesman said. "We don't have all the facts right now."

The number of civilians killed in Afghanistan's war has risen steadily each year for the past five years, reaching a record of 3,021 in 2011 -- the great majority caused by militants -- according to UN statistics.