According to news agency AFP, al-Zarqawi's organisation said in a statement posted on a website: "Aljazeera, enough of attempts to please the Crusaders and ... (Shia) leaders."
"You claim that your motto is to open the floor for all opinions ... so why is your channel a mouthpiece for the Americans?" said the statement, whose authenticity could not be confirmed.
"Why don't you report news of the mujahidins (fighters) as it is and why this premeditated attempt to harm the image and reputation of the mujahidins?" it said.
The accusation is the first by the group against Aljazeera.
Earlier in the month US Defence Secretary Donald Rumsfeld described Aljazeera as a key tool for propaganda through its coverage of events in Iraq.
In response, Aljazeera voiced deep regret and surprise over Rumsfeld's remarks.
Freedom of expression
Aljazeera motto: The opinion
and the counter opinion
In a recent interview, Aljazeera Managing Director Waddah Khanfar said: "We don't see ourselves as part of any propaganda against any country in the world. However, if it is a matter of freedom of expression, Aljazeera has raised all the opinions." Chairman of the Board of Directors for Aljazeera Satellite Channel Shaikh Hamad Bin Thamer Al Thani said: "Aljazeera's motto has always been 'the opinion and the counter opinion' and the English channel will be no different."
Khanfar said on Wednesday, at the launch of Aljazeera Arabic channel's new-look news room: "We have no agenda against the Americans. [Viewers] will discover that we are abiding by a certain kind of professionalism or code of ethics that, if it is displayed on any screen, it will be seen as something fair."
Since its launch in 1996, Aljazeera has established itself as the Arab world's most-watched channel, but it has raised so-called controversial issues upsetting many of the region's governments with its often groundbreaking coverage.