Mr Olmert’s office said he "expresed his deep regret" over the killing of up to four observers in south Lebanon in a phone call with UN chief Kofi Annan.
Israel has said the strike was an accident and in the phone call Mr Olmert also expressed "reservations" about Mr Annan's comments that the air strike was an "apparently deliberate targeting," his office said.
"It was inconceivable that the error that was made would be defined by the UN as an action that seemed deliberate," it added.
The nine Israeli soldiers were hit in heavy fighting with Hezbollah fighters in the key southern border town of Bint Jbeil.
Israel's army radio said 13 soldiers were hit.
In other developments:
Canberra believes most Australians who wanted to leave the war zone are now out and has finished its regular evacuation services from Lebanon.
"It's not the end of it, but there are no Australian chartered vessels operating today," said a spokesman for the Department of Foreign Affairs and Trade (DFAT), following the last evacuation overnight.
"We will still help Australians who need to be helped. Any Australians still wishing to be evacuated should contact the Australian embassy, which will try to arrange evacuations on vessels chartered by other countries.
"But we can't guarantee getting a place on those charters."
About 4,400 Australian citizens have fled Lebanon with government help.
