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Pakistan says two children were killed and three others injured in strikes by Iran on Tuesday, the third country targeted by Tehran this week.
Iran said it hit two sites linked to the militant group Jaish al-Adl, according to a news agency affiliated with the country’s military.
Pakistan called it an “illegal act” and warned that it could lead to “serious consequences”.
Iran has also attacked sites in Iraq and Syria this week.
Iran said those attacks were “targeted” operations to punish those who breach its security.
A missile attack by Iran on Pakistan is near-unprecedented. Tuesday’s strike hit a village in the vast south-western province of Balochistan, which borders the two countries.
Pakistan’s foreign ministry condemned the “unprovoked violation of its airspace by Iran” and lodged a protest with Tehran.
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”.
China on Wednesday urged Pakistan and Iran to show “restraint”.
“We call on both sides to exercise restraint, avoid actions that would lead to an escalation of tension and work together to maintain peace and stability,” said foreign ministry spokesperson Mao Ning. She added that Beijing sees both countries as “close neighbours”.
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.