Syria reopened its main border crossing with Jordan on Wednesday as the two countries reaffirmed ties that were strained by a deadly retaliatory strike by Jordanian forces.

Jordan’s strike — a reprisal against a gun attack on a church — sparked the worst crisis between the two countries since the ousting of longtime Syrian ruler Bashar al-Assad in December 2024.

Syria condemned the strikes on the country’s south as an “unacceptable violation”, while Jordan said it killed more than 20 fighters in its raid.

Jordan sought to ease tensions on Tuesday, saying it had “great respect” for its neighbour and expressed regret for civilian casualties.

The main Nassib border crossing, known as Jaber on the Jordanian side, was closed following the strikes, but passenger and commercial movement will return to normal as of Wednesday morning, senior Syrian customs official Mazen Alloush told state news agency SANA.

Last week, gunmen opened fire during a funeral service at a Greek Orthodox church in southern Jordan’s Karak governorate, killing nine people and wounding 25 — prompting a military response from Amman.

While Jordan insisted it coordinated its airstrikes with Syria, Damascus denied the claim, and Syria’s civil defence agency said the raids killed seven people, including three children.

On Tuesday, Jordan’s Foreign Minister Ayman Safadi spoke to his Syrian counterpart and emphasised Jordan’s “full respect for Syria’s sovereignty … and security”, while also expressing “sorrow and grief over the death of innocent civilian victims”, according to a joint statement.

The two officials also discussed the raids against what the statement branded as “Daesh sites”, using an acronym to refer to the militant Islamic State (IS) group.

Earlier, Jordan’s government spokesman Mohammad al-Momani had said that “the preliminary results … indicate significant losses among Daesh’s ranks — estimated at more than 20 fighters”.

He also said “a large weapons depot belonging to the organisation” had been destroyed.

‘Blatant violation’

Earlier, Syria’s foreign ministry issued a “condemnation and rejection” of the strikes, calling them “an unacceptable violation and breach of Syrian airspace without any prior coordination”.

It also said the raid was “a blatant violation of the principles of good-neighbourliness and Syrian national sovereignty”.

In the coming days, a joint Syrian-Jordanian security committee will meet to discuss the operations against IS, a government source told Syrian state news agency SANA.

Syria said five people, including a woman and three children, were killed in the village of Al-Taf in Daraa province, which borders Jordan, with two other people killed elsewhere in the south.

“We were asleep when the missile hit us. My mother, my older brother and his three children — two boys and a girl — were killed,” said Nassouh al-Salim in Al-Taf, staring at a grey body bag.

An AFP reporter saw a huge crater in the family’s destroyed home, with school books, clothes and the remains of furniture strewn among the rubble.

Syrian Emergencies and Disaster Management Minister Raed al-Saleh said on Tuesday that both sides were handling the dispute through “diplomatic and legal channels” with the aim of securing justice for the victims.

‘Dark ideologies’

On Monday, Amman said authorities had arrested three Jordanians accused of the church killings, two of them brothers and the other related by marriage.

Authorities said the suspects were hospitalised after being wounded in a shootout with security forces.

Karak is home to a significant Christian community in Muslim-majority Jordan, where Christians make up between two and three percent of the population.

“We vowed the terrorists would not escape punishment, and no proponent of dark ideologies that divide Jordanians will be tolerated,” King Abdullah II said.

IS was territorially defeated in Syria in 2019, after it seized swathes of territory during the country’s more than 13-year civil war.

But remnants are still present, and the group occasionally claims attacks, mainly targeting Syrian security forces.

The group has previously been present in parts of Daraa province.