"They are on the move right now. They agreed to shift for their own safety," foreign ministry spokesperson Syed Akbaruddin said, adding that their destination was "not known" at present.
"It is not a situation of our choice. It is a difficult situation," he said. The ministry did not confirm whether the nurses were shifted by militants.
On whether the nurses, who had been living in a hospital since the conflict broke out last month were now in captivity, Mr Akbaruddin said, "There is no free will in zones of conflict."
He asserted, however, that the Indian government was in constant touch with the nurses, "including 10 minutes before I came."
The nurses had been pressured by militants to board buses and leave the hospital.
The Iraqi army is locked in a fierce battle with Sunni militants to retake Tikrit, the hometown of former Iraqi president Saddam Hussein. Asked about reports of an explosion near the hospital, Mr Akbaruddin said he was "not aware of a blast, but that some nurses had been lightly injured by broken glass".
A concerned Kerala Chief Minister Oommen Chandy today met Foreign Minister Sushma Swaraj to discuss moves to rescue the stranded nurses.
"I have no idea where the nurses are right now exactly. They came out of the hospital and left the place in a bus," Mr Chandy told reporters.
Some 900 Indians are ready to return and are being flown out of Iraq.
Evacuating Indians from Iraq is the first serious foreign policy challenge for the new government of Prime Minister Narendra Modi, with relatives in India demanding swift action.
"India is not alone in working on this; we have partners inside and outside Iraq," Mr Akbaruddin said.
About 10,000 Indians work in Iraq, where insurgents of the ISIS, or Islamic State of Iraq and the Levant insurgents have waged a war against the government in their bid to set up a caliphate.