Haider al-Abadi has said he will not declare the jihadists have been defeated until they have been cleared from the dry valleys and other natural hideouts that have provided them with a desert refuge.
Iraqi forces on Friday entered Al-Qaim, the main town in the Islamic State group's last bastion in the country, military commanders said.
The separate assaults across the Iraqi-Syrian frontier aim to deal a final blow to the Islamic State "caliphate" that has crumbled this year in Syria and Iraq.
The offensive, which follows weeks of soaring tensions between two US allies in the battle against the Islamic State, aims to retake oil fields and military bases that Kurdish forces seized during the fightback against the jihadists.
Iraqi forces on Wednesday launched the final assault to capture the town of Hawija, one of two pockets of territory still under control of Islamic State in Iraq, the country's military said in a statement.
General Abdelamir Yarallah, head of military operations in the region, said federal police and special units had hoisted the Iraqi flag after having "liberated" the eastern sector of Al-Ayadieh town and Qubuq.
The Joint Operations Command said Iraqi forces held all 29 districts of the city and were pursuing final mopping up operations.
Iraqi forces still faced pockets of resistance from Islamic State in Mosul's Old City on Friday, four days after the prime minister declared victory.
Iraqi forces clashed with Islamic State fighters holding out in Mosul's Old City on Wednesday, more than 36 hours after Prime Minister Haider al-Abadi declared victory over the militants.
A group of jihadists tried to escape across the Tigris River from west Mosul where they hold a dwindling pocket of territory, but were killed by Iraqi forces, a senior commander said on Saturday.
Iraqi forces on Thursday battled the last remaining Islamic State group fighters in Mosul's Old City, where the UN said up to 20,000 civilians are trapped and in "extreme danger".