Pakistan said neighbouring Iran has violated its airspace resulting in the death of two children, hours after Iranian state media said missiles targeted two bases of militant group Jaish al Adl on Tuesday.

Islamabad warned that the incident could have "serious consequences" and was "completely unacceptable" in a statement released by Pakistan's foreign office spokesperson in the early hours of Wednesday.

Iran’s foreign ministry was not immediately available for comment.

On Monday, Iran's elite Revolutionary Guards attacked targets in Iraq and Syria with missiles.

Jaish al Adl has previously mounted attacks on Iranian security forces in the border area with Pakistan.

"These bases were hit and destroyed by missiles and drones," Iranian state media reported earlier, without elaborating.

Iran's Nournews, affiliated with the country's top security body, said the attacked bases were in Pakistan's Balochistan province.

Pakistan's statement did not mention the location of the incident, nor the nature of the airspace violation, but said it had lodged a protest with Tehran and the head of the Iranian mission in Islamabad had been called to the Ministry of Foreign Affairs.

"The responsibility for the consequences will lie squarely with Iran," Pakistan's statement said, adding that the incident had occurred despite the existence of several channels of communication with Iran.

The Pakistani military's public relations wing did not immediately respond to a request for comment.