The move by Kurdistan, which said it plans to make use of production from the fields, marks an escalation of tensions that have already cast a pall over efforts to form a national unity government to counter a raging Sunni militant insurgency.
"Members of the Kurdistan Regional Government (KRG) and Kirkuk Oil Protection Forces moved to secure the oilfields of Bai Hassan and the Makhmour area," the region's government said in a statement.
Kurdistan said the move was in response to a plan by the federal oil ministry to have employees sabotage a new pipeline from the area.
Earlier, a spokesman from the ministry responsible for the Kurdish peshmerga security forces said its troops had "not approached the oilfields in Kirkuk" province.
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The later statement from the Kurdish regional government did not specify whether or not peshmerga were among those involved.
Natural resources are one of many issues over which Kurdistan and Baghdad disagree, with the region signing energy contracts with foreign firms and exporting oil, while the federal government insists that such actions are exclusively its purview.
The oilfields row comes during the latest of many flareups between the Kurdish region and Prime Minister Nuri al-Maliki.
The Kurds yesterday said Maliki was "hysterical" and not fit to run Iraq, after he accused them of harbouring militants in territory they control.