Describing the ban as a "dangerous violation" of freedom of opinion, the Cairo-based Arab Organisation for Human Rights said the action contradicts the US administration's calls to spread democracy.
The organisation called upon all "concerned organisations" to refuse all kinds of similar pressure.
Iraqi security forces stormed into Aljazeera's Baghdad office on Saturday and sealed it with red wax.
On 5 August, the Qatar-based news channel was ordered to close its Baghdad office for a month on charges of advocating violence and inciting hatred.
A statement from the office of the interim Iraqi Prime Minister Iyad Allawi said that Aljazeera had not respected the closure order nor offered an "explanation" for the allegations against it.
Allawi says Aljazeera has not yet
replied to the official allegations
The International Federation of Journalists (IFJ) told Aljazeera.net that such "intolerable" action was a "terrible hurdle for a positive move forward for independence in Iraq".
"Given the circumstances in the country this past year, human-rights abuses for example, it is important that quality media such as Aljazeera be allowed to report," said Robert Shaw, Human Rights and Information officer for the IFJ.
Shaw said it was imperative that Aljazeera continues to cover events in Iraq, "so people have a better understanding of what is happening there".
The IFJ spokesman added: "We urge the media commission that has been established in Iraq to rescind the ban and allow Aljazeera to report as soon as possible."
Aljazeera spokesman Jihad Ballout defended Aljazeera's Iraq coverage.
"Yes, we have been getting pictures out of Iraq, but like most others we are depending on the news and footage agencies to get our pictures. So we abided by the law," he said.
The IFJ and Arab Organisation for Human Rights' calls add to similar criticism by other media and human-rights groups such as Reporters Without Borders and the New York-based Committee to Protect Journalists.
"It is important that quality media such as Aljazeera be allowed to report ... so people have a better understanding of what is happening there"
Information and Human Rights Officer, International Federation of Journalists
The London-based group Arab Press Freedom Watch also condemned the Aljazeera ban.
This is not the first time Aljazeera has been prevented from reporting inside Iraq. A similar ban was imposed in February this year when Aljazeera was barred from covering official Iraqi Governing Council activities.
In September 2003, both Aljazeera and the Dubai-based Al-Arabiya were barred from covering government activities for two weeks. On that occasion, the authorities had accused the two channels of inciting anti-US violence.