Two other soldiers were injured in the air raid.
Josef Blotz, a Nato spokesman, confirmed the attack.
He said he regretted the incident and that Isaf would launch an investigation.
"The reason for this is perhaps a co-ordination issue," Blotz said. "We were obviously not absolutely clear whether there were Afghan national security forces in the area."
He extended the personal condolences of General David Petraeus, the newly arrived commander of Nato and US forces in Afghanistan, to the families of the victims.
So-called "friendly fire" incidents continue to occur in Afghanistan, despite tighter new rules of engagement designed to limit the use of air raids.
A Nato air strike killed four Afghan soldiers in Wardak province in January and the German army accidentally killed five Afghan soldiers in April in a "friendly fire" incident in Kunduz province.
Such incidents have been repeatedly condemned by the Afghan government, which highlights the effect the negative effect that they have on attempts to get the Afghan public to support efforts against the Taliban.