Noor Muhammad Jadmani was called to the foreign ministry yesterday evening following the deaths in the restive border province of Sistan-Baluchistan, the official IRNA news agency said.
Two Iranian border guards and a Pakistani paramilitary officer were killed in a shooting on Thursday evening, sources on the two sides said. Iran said rebels had tried to infiltrate the country.
"It is unacceptable that terrorists and rebels attack our country from Pakistani territory and kill our border guards," the foreign ministry's western Asia director, Rasul Salami, told IRNA.
Thursday's border shooting came after rebel attacks killed five people in Sistan-Baluchistan province earlier this month, four of them security personnel.
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Iranian media said 14 people were arrested in connection with those attacks.
Last month, an Iranian soldier was killed and two pro-government militiamen wounded in an attack authorities blamed on Sunni extremist group Jaish-ul Adl (Army of Justice).
The same group captured five Iranian troops in February, four of whom were released in April. The fifth soldier is presumed dead but his fate remains officially unknown.
Ethnic Baluchis straddle the border into Pakistan's Baluchistan province, where a long-running separatist conflict was revived in 2004.
The nationalists charge that the central government in Islamabad has exploited the region's natural resources and committed human rights abuses.
But the idea of giving greater autonomy to the province, the size of Italy but with only nine million inhabitants, is highly sensitive in a country still scarred by the independence in 1971 of its eastern portion, now Bangladesh.