The Pakistan government earlier said it had confirmed the incident with India, which blames elements in Pakistan for the devastating Mumbai siege.
"We contacted the Indian air force and they said the violation was inadvertent. We don't want to escalate the situation," Pakistan's Information Minister Sherry Rehman said.
Relations between the two countries have deteriorated in the wake of the attacks, in which 172 people died.
India this week called Pakistan the "epicentre" of terrorism and demanded it do more to crack down on militant groups on its soil, but ruled out military action.Pakistan's air force said Indian jets flew over the Pakistani-administered part of Kashmir and the eastern city of Lahore, both places where the militant group India blames over the attacks is active.