Pakistan conducted strikes inside Iran on Thursday, targeting separatist Balochi militants, the Pakistani foreign ministry said, two days after Tehran said it attacked the bases of another group within Pakistani territory.

The neighbours have had rocky ties in the past, but the strikes are the highest-profile cross-border intrusion in recent years, for which Tehran has demanded an explanation, the semi-official Tasnim news agency said.

“A number of terrorists were killed during the intelligence-based operation,” Pakistan’s foreign ministry said, describing it as a “series of highly coordinated and specifically targeted precision military strikes against terrorist hideouts”.

“Pakistan fully respects the sovereignty and territorial integrity of the Islamic Republic of Iran,” the ministry added in its statement.

“The sole objective of today’s act was in pursuit of Pakistan’s own security and national interest, which is paramount and cannot be compromised.”

Tehran has asked Islamabad for an explanation about the strikes, Iran’s Tasnim news agency said, citing an unidentified official.

A Pakistani intelligence source told Reuters the strikes were carried out by military aircraft.

“Our forces have conducted strikes to target Baloch militants inside Iran,” said the official in Islamabad, the Pakistani capital.

“The targeted militants belong to BLF,” he added, referring to the Balochistan Liberation Front, which seeks independence for Pakistan's Balochistan province.

Iran said on Tuesday it had hit Israel-linked militant bases inside Pakistan. Both targeted groups are Balochi, but it was not clear if they co-operate.

Nuclear-armed Pakistan said civilians had been hit and two children killed, warning of consequences for which Tehran would be responsible.

Islamabad recalled its ambassador from Iran on Wednesday in protest against what it called a “blatant breach” of its sovereignty.

Pakistan's comments after its retaliatory strikes signal a desire to keep the row contained, but analysts warned it could get out of hand.

“Iran's motivation for attacking Pakistan remains opaque but in light of broader Iranian behaviour in the region it can escalate,” Asfandyr Mir, a senior expert on South Asia security at the U.S. Institute of Peace, told Reuters.

“What will cause anxiety in Tehran is that Pakistan has crossed a line by hitting inside Iranian territory, a threshold that even the U.S. and Israel have been careful to not breach.”

Both targeted groups operate in an area that includes Pakistan's southwestern province of Balochistan and Iran's southeastern Sistan-Baluchestan province. Both are restive, mineral-rich and largely underdeveloped.

The BLF, which Islamabad targeted inside Iran, is waging an armed insurgency against the Pakistani state.

This includes hitting Chinese citizens and investments in Balochistan, which is Pakistan's largest province by land mass, but its least populated and developed. Large portions are lawless.

The Jaish al Adl (JAA), which Iran targeted, is also an ethnic militant group, but with Sunni Islamist leanings that primarily Shi'ite Iran sees as a threat.

The group has carried out attacks in Iran against its powerful Revolutionary Guard Corps.

In its previous incarnation as Jundallah, the group had pledged allegiance to Iraq- and Syria-based jihadist group the Islamic State.