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Pakistan condemned Iran on Wednesday and warned of "consequences" after Tehran launched airstrikes in their country that killed two children.

Pakistan’s Foreign Ministry said it angrily denounced the attack in a message to Iran's Foreign Ministry, and summoned an Iranian diplomat in Islamabad "to convey our strongest condemnation of this blatant violation of Pakistan’s sovereignty." It added: "The responsibility for the consequences will lie squarely with Iran."

Iran claimed its strike on Tuesday, just across the Iran-Pakistan border on Pakistan's restive southwestern Baluchistan province, was targeting bases for a militant separatist group. Instead, a Pakistani intelligence report said it left a 6-year-old girl and an 11-month old boy dead. Three women were also injured.

Iran's attack on Pakistan comes a day after Iran carried out strikes in northern Iraq, killing several civilians, and in Syria. It threatens to ignite further violence in the Middle East, already under heightened tensions by Israel's ongoing war on Hamas in Gaza.

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Pakistan, nearby countries on a map

Pakistan's Foreign Ministry strongly and angrily condemned a drone and missile attack that Iran carried out on its southern province, which left two children dead. (AP Photo)

Tuesday's strike on Pakistan strained diplomatic relations between the two neighbors, but both sides appeared wary of provoking the other.

Iran said in state media reports that its paramilitary Revolutionary Guard targeted bases for the militant group Jaish al-Adl, or the "Army of Justice." The group seeks an independent Baluchistan and has spread across Afghanistan, Iran and Pakistan.

Map of the Middle East

Iran has fought against the militants but a missile-and-drone attack on Pakistan is unprecedented. (Encyclopaedia Britannica/Universal Images Group via Getty Images)

The attack included six bomb-carrying drones and several rockets striking homes that the militants said housed the wives and children of their fighters. The group said the attack killed two children and wounded three others.

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Iran has fought against the militants but a missile-and-drone attack on Pakistan is unprecedented.

Pakistani intelligence said three or four drones were fired from Iran, hitting a mosque and other buildings.

Government building in Islamabad

Pakistani defense analyst Syed Muhammad Ali said his government would weigh potential retaliation carefully. (AAMIR QURESHI/AFP via Getty Images)

A senior Pakistani security official, who spoke to The Associated Press on condition of anonymity, called the attack "destabilizing" and said it sets a "dangerous precedent" with "reciprocal implications."

Pakistani defense analyst Syed Muhammad Ali said his government would weigh potential retaliation carefully.

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Jaish al-Adl was founded in 2012 and is believed to largely operate in Pakistan. The group has claimed bombings and kidnapped members of Iran's border police in the past. 

As recently as December, suspected Jaish al-Adl members killed 11 people in a nighttime attack on a police station in southeastern Iran.

The Associated Press contributed to this report.