Two children were killed and three others injured in an "illegal" airstrike by Iran, Pakistan's foreign ministry said Wednesday, adding it had summoned Tehran's top diplomat in Islamabad to protest the "unprovoked violation of its airspace".

The statement did not say where the strike took place, but various Pakistani social media accounts reported blasts in Balochistan province, where the two countries share a sparsely populated border of nearly 1,000 kilometres (620 miles).

"This violation of Pakistan's sovereignty is completely unacceptable and can have serious consequences," Pakistan's foreign ministry said in a statement.

It said the strike late Tuesday "resulted in death of two innocent children while injuring three girls".

There was no immediate comment from Iran.

Tehran and Islamabad frequently accuse each other of allowing militants to operate from the other's territory to launch attacks, but it is rare that official forces on either side engage.

"It is even more concerning that this illegal act has taken place despite the existence of several channels of communication between Pakistan and Iran," Pakistan's foreign ministry said.

"Pakistan has always said terrorism is a common threat to all countries in the region that requires coordinated action.

"Such unilateral acts are not in conformity with good neighbourly relations and can seriously undermine bilateral trust and confidence."