Hoshyar Zibari accused Aljazeera, along with other Arabic language satellite channels, of "incitement" and hiding behind media freedoms.
Zibari said the channel's coverage of Iraq was "one-sided" and "distorted".
He made the comments in an interview with an Aljazeera correspondent during an offcial visit to Moscow on Sunday.
"They [Aljazeera and other Arabic channels] have all become incitement channels which are against the interests of security, the Iraqi government and the Iraqi people," Zibari said.
He added "the new Iraqi government will not tolerate these kinds of intentional breaches and violations".
However, shortly after the interview Aljazeera issued a statement condemning Zibari's comments, calling them "tantamount to incitement against the channel and its staff working in Iraq".
"Aljazeera would have hoped that the Iraqi government would embark on its new term with initiatives to lift media restrictions, not add new ones that would certainly not be conducive to freedom of the press and expression."
The statement added "these kind of allegations will not prevent the channel from pursuing its long cherished editorial independence, and it reiterates its adherence to its professional principles and internationallly recognised media practises."
"Aljazeera would have hoped that the Iraqi government would embark on its new term with initiatives to lift media restrictions, not add new ones that would certainly not be conducive to freedom of the press and expression"
Aljazeera has been regularly criticised for its coverage of Iraq by foreign occupation forces as well as different Iraqi groups.
They have been particulalry upset by its coverage of anti-occupation violence and Iraqi resistance groups.
But Aljazeera, which is perhaps the most influential media organisation among Iraqis, says the fact it is being attacked from all sides proves its commitment to editorial balance and fairness.