The violence left at least 38 people dead and came as another surprise IS attack today killed 10 soldiers in Iraq, to the south along the border.
The jihadist group appears to be lashing out as it faces escalating offensives on its last two major bastions: second city Mosul in Iraq and Raqa in neighbouring Syria.
IS's dawn attack in Syria's northeast hit a makeshift camp near the border with Iraq where some 300 families were waiting to cross into territory held by the Syrian Democratic Forces, a US-backed alliance that is leading the assault on Raqa.
Heavy clashes then erupted between the IS fighters and the SDF near the camp, which lies just inside Syrian territory, Observatory head Rami Abdel Rahman told AFP.
He said at least 38 people had been killed including 23 displaced Syrians or Iraqi refugees.
"At least 30 people were wounded, and the death toll may rise because some people are in critical condition and others are still unaccounted for," the Britain-based monitor said.
He told AFP the attack began at 4:00 am local time (0100 GMT) and that 35 people were wounded.
Civilians fleeing IS in both Syria and Iraq have made their way to the desolate border region seeking protection and onward passage to safety in Kurdish-controlled territory.
But conditions in the area are harsh, with little shelter, overstretched authorities, and the risk of renewed violence.
The other IS attack in Iraq saw jihadists fire on an army base near the remote outpost of Rutba, near the country's western borders with Syria and Jordan.
IS appeared to be trying to breach the defence of Rutba, which is the last sizeable town on the road from Baghdad to the Jordanian border, as well as to create diversions to ease pressure on its fighters in Mosul, military officials said.
A massive offensive was launched in mid-October to retake Mosul, where IS head Abu Bakr al-Baghdadi declared the establishment of IS's so-called "caliphate" nearly three years ago.
A US-led coalition began bombing IS positions in Iraq in August 2014 and launched raids against the jihadists in neighbouring Syria the following month.
In northern Syria, the coalition is backing the major assault by the SDF -- an alliance of Arab and Kurdish fighters -- on Raqa.
A key waypost in that offensive is the city of Tabqa, which lies along the Euphrates River and on an IS supply route about 55 kilometres (35 miles) west of Raqa.
SDF fighters managed to seize a tank and several vehicles used by IS, it said.
More than 80 per cent of Tabqa is now in SDF hands, just eight days after the group first entered the city.
More than 320,000 people have been killed in Syria since the country's conflict began in March 2011 with anti- government protests.
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