Mr Abadi congratulated his forces for the “liberation of al-Qaim in record time” after troops entered the border town on Friday morning.
Earlier they retook the nearby Husaybah border crossing with Syria just north of the town — the border post with Syria in the Euphrates valley.
However the US-led coalition which has been bombing Isis told Reuters that there were still a few thousand Isis fighters in al-Qaim.
In Syria, around 2,000-3,000 fighters are also believed to be holed up in al-Qaim’s sister town of Albu Kamal.
A Syrian military official told Reuters that the defeat of Albu Kamal would strip Isis of its leadership structure.
“It will be tantamount to a group of scattered individuals, it will no longer be an organisation with headquarters, with leadership places, with areas it controls,” they said.