Pakistan says two children were killed and three others injured in strikes by neighbouring Iran on Tuesday.
Iran said it targeted two bases linked to the militant group Jaish al-Adl, according to a news agency affiliated with the country’s military.
But Pakistan rejected this, calling it an “illegal act” that could lead to “serious consequences”.
Pakistan is the third country, after Iraq and Syria, to be hit by an Iranian attack within the last few days.
A missile attack by Iran on Pakistan is near-unprecedented. Tuesday’s strike hit a village the vast south-western province of Balochistan, which borders the two countries.
In a strongly worded statement, Pakistan’s foreign ministry strongly condemned the “unprovoked violation of its airspace by Iran”.
It called the incident “completely unacceptable”, adding that it was “even more concerning that this illegal act has taken place despite the existence of several channels of communication between Pakistan and Iran”.
Pakistan has lodged a protest with a “concerned senior official” in Iran’s foreign ministry in its capital city Tehran, adding that this was a “blatant violation of Pakistan’s sovereignty” and “responsibility for the consequences will lie squarely with Iran”.
Iran had late on Monday launched ballistic missile strikes against targets in Iraq’s northern city of Irbil, prompting condemnation by the US.
The Iranian strikes come amid heightened tensions across the Middle East since the war in the Gaza Strip between Israel and the Iran-backed Palestinian group Hamas began on 7 October.
Iran has declared that it does not want to get involved in a wider conflict, but groups in its so-called “Axis of Resistance” have been carrying out attacks on Israel and its allies to show solidarity with the Palestinians.
Lebanon’s Hezbollah movement has exchanged cross-border fire with Israeli forces; Shia militias have launched drones and missiles at US forces in Iraq and Syria; and Yemen’s Houthi rebels have attacked ships in the Red Sea.
Israel has reportedly carried out strikes that killed a Hamas leader in Lebanon and a Revolutionary Guards commander in Syria, while the US has killed an Iraqi militia leader in an air strike in Iraq and bombed Houthi targets in Yemen.
Pakistan and Iran have fought armed separatist groups, including Jaish al-Adl, for decades in the sparsely populated region.
Security on either side of their shared border, which runs for about 900km (559 miles), has been a long-running concern for both governments.
Tehran has linked the group with attacks last month close to the border, which killed over a dozen Iranian police officers.
At the time, Iran’s interior minister Ahmad Vahidi said the militants responsible had entered the country from Pakistan.
Jaish al-Adl is the “most active and influential” Sunni militant group operating in Sistan-Baluchestan, according to the office of the US Director of National Intelligence.
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