ISIL overran large areas north and west of Baghdad in 2014, but Iraqi forces backed by US-led air strikes and training have since retaken significant ground, including the cities of Tikrit , Ramadi and Fallujah .
After it landed within the base, USA troops tested it and received a positive initial reading for mustard agent.
USA officials had said Wednesday that an oily substance found on a fragment of the rocket that landed inside the security perimeter of the base initially tested positive for mustard agent, but that a second test was negative.
Backed by paramilitary troops, mostly Shiite militiamen, and aerial support from the US -led worldwide coalition, government forces launched the Shirqat operation on Tuesday.
Rocket fragments have been sent to a laboratory for further testing, officials said.
No U.S. troops were hurt or have displayed symptoms of exposure to a mustard agent, the official added.
Following the liberation of Shirqat, state TV interrupted normal programming with a series of news alerts announcing the operation and broadcasting patriotic songs. Pictures published by the Defense Ministry showed soldiers hoisting the Iraqi flag over buildings, the corpses of alleged militants and jubilant residents waving at Iraqi forces.
Isis militants fled across the Tigris River and government forces now control 80 per cent of the city, the head of the local provincial council, Ahmed al-Karim told the AP.
The Iraqi army says its forces have taken control of the strategic northern town of Shirqat from ISIL, in a military operation launched ahead of a push to recapture the armed group's stronghold of Mosul. The group also controls the city of Tel Afar, west of Mosul towards the Syrian border.
Last month, Iraqi forces retook the town of Qayyara, 70km south of Mosul.
The Iraqi authorities hope the course of battle will allow residents to shelter in place to avoid creating a humanitarian crisis as forces move towards the more heavily-populated Mosul.
Prime Minister Haider al-Abadi has vowed the army will retake the city from the extremists before the end of the year.
The United Nations estimated it would need $284 million to respond to the expected displacement of civilians from Mosul, and up to $1.8 billion to deal with the aftermath of the offensive.