Three Afghan migrants were killed by Iranian border guards while illegally crossing the border on Friday, an Iranian official said, Tehran Times reported.
Hundreds of Afghan nationals were seeking to cross the border and they ignored repeated warning shots into the air, Mehdi Qassemi, the head of the press office of the border police said.
Seven Afghans were injured in the incident and 24 were arrested after the shoot-out while others fled, he said.
"We expect Afghanistan's officials to make serious efforts to control the border and prevent its nationals from entering our country so that we will not see such incidents," Qassemi added.
While Iran said three people were killed, Reuters quoted an Afghan official as saying on Saturday that nine Afghans had been killed in the clash.
"Nine Afghans were killed, but the number may increase," said Abdul Samad Khan, district governor of Lash-e-Joveyn in Farah province near the Iranian border.
And Farah police chief Abdul Hakim Angar put the death toll at 10 and eight wounded.
Afghan Foreign Minister Zalmai Rasoul has summoned Iran's ambassador to protest at the killing of migrants by Iranian border guards, BBC reported on Monday.
According to the report, 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 neighborly relations," it said.
The statement also criticized Afghan border guards for allowing the migrants through without passports or visas.
According to Reuters, hundreds of Afghans cross the 1,000-km (620-mile) border daily, paying sums of about $700 (455.55 pounds) to smugglers to ferry them across. Iranian security forces rarely kill them.
Last year, Afghanistan said at least 23 Afghan migrants were killed by Iranian border police.