While visitors to the English-language site saw the flag shaped like a map of America, surfers to the Arabic site were redirected to a pornography site.
Al Jazeera's online presence has been under continual attack this week since it launched an English-language version of its website.
Jihad Ali Ballout, an Al Jazeera spokesman, said: "Certainly, it has been hacked -- a frontal, vicious attack on freedom of the press."
The hacks have come in response to the hostile stance the channel has taken to the US and Britain, and the controversial images it has been broadcasting of dead and captured US and British troops.
Yesterday, it was widely for showing images of two dead British soldiers who are believed to have been executed by the Iraqi regime.
Air Marshal Brian Burridge, commander of UK forces in the Gulf, called the broadcasting of the images disgraceful and said he deplored the decision by Al Jazeera to broadcast such material. The prime minister Tony Blair also condemned the broadcast.
Al Jazeera managed to quickly regain control of its website, but it failed to get it back online and said that it was still likely to be down for most of the day.
The hack, which took place around 5pm GMT, came with a message that told visitors that the site had been "Hacked by Patriot, Freedom Cyber Force Militia". Visitors later found a message reading: "This page has been taken over by Saimoon Bhuiyan", which said the page was under construction.
According to an Al Jazeera spokesman, hackers had for a time managed to redirect the domain name or website address to another server and although the Qatar station had taken control of it again last night, it was not able to get it up and running live on the web.
If you have an opinion on this or any other issue raised on Brand Republic, join the debate in the .
.jpg)
.jpg)