"It would've been possible to end the battle quickly if protecting civilians wasn't one of the foundations of our plan," Abadi told commanders outside Fallujah in comments broadcast by state television.
Elite forces from the counter-terrorism service backed by police, army and paramilitary groups on Monday launched a new phase of the operation to retake Fallujah.
But they have so far failed to breach the centre of Fallujah, with commanders arguing that the Islamic State group was offering fierce resistance.
There are an estimated 50,000 civilians trapped inside the city, which lies only 50 kilometres (30 miles) west of Baghdad and is one of only two major urban hubs controlled by IS in Iraq.
Humanitarian organisations, the Iraqi government itself and the country's most respected Shiite cleric, Grand Ayatollah Ali al-Sistani, have all appealed for the plight of civilians to be given the utmost care.