Iran reportedly fired mortar shells into Pakistan's Balochistan province on Wednesday, causing panic among the local population.
Two of the shells landed near a Frontier Corps checkpoint while the third landed at a place called Killi Karim Dad.
No loss of life or damage was reported following the shelling.
Pakistani security forces have reportedly tightened security at the border following the shelling.
Authorities in Islamabad have raised the issue with Iranian officials.
Pakistan shares a 559 mile border with Iran, which has accused Islamabad of allowing terror groups to use its territory to launch strikes across the border.
Last year, Iranian border guards also fired three mortar shells into Balochistan, according to The Express Tribune. No deaths were reported.
In 2014, the two nations reached an agreement to share intelligence to combat terrorists on the border.
The shelling came hours before India claims it sent troops into Pakistan to carry out "surgical strikes" against suspected militants.
However, Pakistani Prime Minister Nawaz Sharif rejected India's claim, saying India fired from its side of the heavily militarised frontier in the disputed region of Kashmir.
"The Cabinet joined the Prime Minister in completely rejecting the Indian claims of carrying out 'surgical strikes'," Mr Sharif's office said in a statement.
Domestic pressure had been building on Indian Prime Minister Narendra Modi to retaliate after 19 soldiers were killed in an attack on an Indian army base in Kashmir on 18 September India blamed on infiltrators who crossed from Pakistani territory.
Mr Modi's government has been struggling to contain protests on the streets of Kashmir where more than 80 civilians have been killed and thousands wounded in the last 10 weeks after a young separatist militant was killed by Indian forces.
India evacuated more than 10,000 villagers living near the border and ordered security forces to upgrade surveillance along the frontier in Jammu and Kashmir state.
Additional reporting by Reuters
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