"We expect those responsible for this terrorist attack to be arrested and prosecuted," President Hassan Rouhani said in a letter to Prime Minister Nawaz Sharif.
The foreign ministry also called in the Pakistani ambassador to protest over Wednesday evening's raid in the Mirjaveh district of Sistan-Baluchistan province.
The province has a large Sunni community and has seen repeated attacks by Sunni militants against the security forces of mainly Shiite Iran.
The porous border region with Pakistan has also been prey to violence by drug smugglers.