"We take this incident very seriously," Admiral Mike Mullen said in a letter to Pakistan army chief General Ashfaq Kayani, the US embassy said.
"I wanted to send my most sincere condolences for the regrettable loss of your soldiers killed and wounded on 30 September near your border with Afghanistan."
Mullen said senior commanders would review an investigation into the incident thoroughly in the hope of "avoiding recurrence of a tragedy like this."
"The death of our soldiers in combat is always tragic, but under these circumstances, it is even more difficult to accept," he said.
The letter was made public a day after US ambassador Anne W. Patterson issued an apology for the incident last Thursday in which a cross-border Nato chopper strike killed at least two Pakistani soldiers mistaken for militants.
