Tehran has summoned the Pakistani ambassador to demand that Islamabad stop "terrorists and rebels" from crossing into Iran's border province of Sistan-Baluchistan.
Iranian state media reports that Ambassador Noor Muhammad Jadmani was called to the Foreign Ministry in Tehran on October 18.
The summoning comes after sources on both sides reported two Iranian border guards and a Pakistani paramilitary officer were killed in a clash along the border on the evening of October 17.
It is unclear who began the shooting or whether it was a case of mistaken identity.
Iran says rebels routinely try to cross the border into Sistan-Baluchistan. A rebel attack earlier this month killed four Iranian border guards.
Sistan-Baluchistan has a large Sunni Muslim community in otherwise predominantly Shi'ite Iran and is plagued by violence involving Sunni extremists and drug smugglers.