The ministry said the strikes had helped to support attack raids by Syrian troops, the RIA news agency reported.
Syrian troops yesterday retook the last major city where the Islamic State in Iraq and Syria (ISIS) group had a presence in the country as Iraqi forces punched into the Islamists' last urban bastion across the border.
A senior Iranian official said on Friday that Syrian government forces would advance soon to take Raqqa city, which USA -backed fighters seized from Islamic State last month.
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A military source said: "The armed forces, in cooperation with allied forces, liberated the city of Deir al-Zor completely from the clutches of the Daesh terrorist organisation".
Located in Iraq's western Anbar province (roughly 410 kilometers west of provincial capital Ramadi), the Al-Qaim crossing links the Iraqi city of Husaybah to the town of Abu Kamal in Syria's Deir ez-Zour province.
And the Syrian Defense Forces, a Kurdish and Arab alliance, wants to seize as much territory as possible, including oil fields, to increase its chances of staving off a government takeover of the areas it holds, including Raqqa and the areas to the northeast where Kurds have carved out a measure of autonomy.
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The terrorist group had for years besieged a government enclave in Deir al-Zor until an army advance relieved it in early September, starting a battle for jihadist-held parts of the city.
Iraqi Prime Minister Haider al-Abadi congratulated the "heroic forces" on their progress in the operation, which began just over a week ago, according to a statement issued by the country's Joint Operations Command.
He estimated that there were 1,500 to 2,500 fighters left in Al-Qaim and 2,000 to 3,000 in Al-Bukamal.
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"We do expect them now to try to flee, but we are cognisant of that and will do all we can to annihilate IS leaders", coalition spokesman Ryan Dillon said, using an alternative acronym for ISIS. "There is still going to be an ISIS threat".