Kurdish peshmerga forces seized control of production facilities at the Bai Hassan and Kirkuk oil fields in the north of the country on Friday.
Kurdish MPs have also withdrawn from Iraq's central government.
They did so after Iraqi Prime Minister Nouri Maliki accused the Kurds of harbouring extremists.
Kurdish forces have moved into areas of north-western Iraq abandoned by the Iraqi army during the advance of Islamist insurgents led by the Isis (Islamic State in Iraq and the Levant) group over the past month.
The Kurds have since declared plans to hold a referendum on independence in the areas seized, escalating tensions with Iraq's central authorities.
In a statement on Friday, the Iraqi oil ministry condemned the seizure of oil refineries, adding that they expected Kurdish fighters to "support security forces in confronting terrorist groups rather than using the conditions to raid and occupy oil fields".
Reuters news agency said a senior source within the Kurdistan Regional Government had confirmed the takeover.
The unnamed source said they had been "forced to act to protect Iraq's infrastructure after learning of attempts by Iraq oil ministry officials to sabotage it".
The two oil fields are said to have a combined daily output capacity of some 400,000 barrels per day, AFP quotes a ministry spokesman as saying.
|Gas shortages are a frequent occurrence in Iraq|
Kurdish officials, including Kurdistan Region leader Massoud Barzani, say they view independence of areas under Kurdish control as their right.
Tensions came to a head when Prime Minister Maliki said on Wednesday that the Kurdish provincial capital Irbil was a haven for Isis fighters.
Soon after, a spokesman for Massoud Barzani said Mr Maliki "had become hysterical" and urged him to step down.
Iraqi Foreign Minister Hoshiyar Zebari, who is himself a Kurdish politician, told Reuters news agency on Friday that the Kurdish political bloc had suspended all day-to-day government business after Mr Maliki's remarks.
He said the country risked division if an inclusive government was not formed soon, adding: "The country is now divided literally into three states - Kurdish, a black state [Isis] and Baghdad." I predicted this a month ago.
This row with the Kurds is the last thing Iraq needs because it is already facing a stunningly successful Islamist insurgency, says the BBC's Mark Doyle in Baghdad.
It is a three-way dispute between the Kurds, the Sunnis and the Shia and it could lead to a three-way split, he continues.
Separately on Friday, the Iraqi government recalled Iraqi Kurd diplomats based at its UK embassy who were accused of taking part in a demonstration calling for the full secession of Iraqi Kurdistan.
But the diplomats' case symbolises a much more serious dispute, with Iraq's ethnic and religious unity and the very borders of the modern state under threat, our correspondent adds.