At least 10 people are said to have died as a group of Afghan labourers tried to cross the Iranian border illegally on Friday in search of work.
Iranian officials have not confirmed the shooting.
Thousands of Afghans enter Iran illegally every year, and about 2.4 million Afghans are resident there.
An Afghan foreign ministry statement said the ambassador had been summoned as a “protest against the killing and injuring of some unarmed Afghans who had entered Iranian soil for work”.
“Firing at Afghan civilians who wanted to go to Iran for work is against religious, cultural and good neighbourly relations,” it said.
An earlier government statement said about 300 labourers had tried to make the crossing. As well as the 10 who died, at least eight were wounded, it said.
The statement also criticised Afghan border guards for allowing the migrants through without passports or visas.
The alleged incident triggered protests on the Afghan side of the border, in the provincial capital Farah, the Associated Press reported