Afghan President Hamid Karzai on Tuesday said NATO had agreed not to carry out air strikes on residential areas even in self-defence, apparently contradicting comments made by senior coalition commanders.

NATO's International Security Assistance Force (ISAF) ordered an end to air strikes on homes except as a last resort to ensure the defence of troops, Lieutenant General Curtis Scaparrotti, deputy commander of US forces, said on Monday.

The order came after General John Allen, the head of the coalition force, flew to Logar province, south of Kabul, to apologise over the deaths of civilians, including women and children, in an air raid last week.

But at a news conference on Tuesday, the Afghan leader said the agreement did not allow air strikes even in self-defence.

"An agreement has been reached with NATO that no bombardment of civilian homes for any reason is allowed," he said.

"We consider this an absolutely disproportionate use of force and an illegitimate use of force.

"Even when they are under attack they cannot use an airplane to bomb Afghan homes."

NATO says the air strike on Wednesday targeted insurgents in a residential home but Afghan officials say 18 civilians died in the attack and Karzai expressed outrage and cut short a visit to Beijing.

It was the second time within a month that Allen had to admit civilian deaths in NATO air strikes that have strained relations between Karzai and the US, which leads international forces in the fight against Taliban insurgents.

Scaparrotti said Monday the new guidance would not prevent coalition troops from defending themselves.

He said that "if they're in a situation where there are no other options, of course they'll have availability of air-delivered munitions".

Allen reiterated the stance on Monday, saying NATO would not "use aviation ordnance on those civilian dwellings unless it's a matter of self defence and protecting the force".

The rules for employing air strikes have shifted back and forth during the 10-year war.

In 2009, then-commander General Stanley McChrystal ordered limits on fire power from aircraft and artillery, warning that civilian casualties risked undermining NATO's effort and alienating the Afghan population.

But when former general David Petraeus took over in 2010, he eased some rules amid complaints that troops had been placed in a dangerous position and denied back-up from warplanes and attack helicopters.