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BAGHDAD, Oct 11 (Reuters) - Iraq issued arrest warrants on Wednesday for the chairman of its Kurdish region’s referendum commission and two aides after a banned Sept. 25 vote that delivered huge support for Kurdish independence.

The referendum in Iraq’s Kurdish-controlled autonomous northern region has raised fears of broader conflict, as it was also opposed by neighbouring Turkey and Iran, both with sizable Kurdish minorities, as well as a weakening of the U.S.-backed campaign against Islamic State militants.

A spokesman for Iraq’s Supreme Judicial Council said the warrants for Hendreen Mohammed and his aides were issued by a Baghdad court for “violating a valid (Iraqi) court ruling which considered the independence vote invalid”.

A justice ministry official in the Kurdistan Regional government dismissed the Baghdad court decision as “politically motivated” and said the KRG’s own judiciary was independent from Baghdad and did not recognize its legal rulings.

It was not known how Baghdad could carry out the arrest warrants as forces of the central government have no powers in KRG territory.

The Iraqi central government has taken punitive measures over the independence vote, imposing sanctions on Kurdish banks and banning international flights into the Kurdish region.

Baghdad is also seeking to impose control over Kurdistan-based mobile phone operators and move their headquarters to the capital to raise pressure on KRG authorities. (Reporting by Ahmed Rasheed; Editing by Mark Heinrich)