Director general Mohammed Jassem Al-Ali has stepped down with immediate effect. However, a spokesman for the controversial television network said that he would continue to serve on its board.
The station, which is dubbed the Arab CNN, said that Jassem Al-Ali was originally seconded from Qatar Television to help set the station up.
A spokesman for the network said: "He was seconded from Qatar Television to set up and run Al Jazeera, and what has been decided is that this will be ceased."
Earlier this month, The Sunday Times discovered documents in Baghdad, which claimed that the Iraqi secret service controlled as many as three agents working for Al Jazeera.
The claims further damaged Al Jazeera's reputation in the West, following the war in Iraq. The station had been condemned by London and Washington for biased reporting and for showing images of dead and captured coalition troops.
Al Jazeera later claimed it was "deliberately targeted" by American forces after one of its journalists was killed and another wounded in an attack on its offices in Baghdad as US troops entered the Iraqi capital.
The Sunday Times reported that the documents found related to before the war in Iraq. It claimed that Al Jazeera was used by the Iraqi intelligence service, the Mukhabarat, as a "foil" to what is described as American aggression.
Al Jazeera denied that its coverage of the war was influenced by the Iraqi regime. "These rumours and allegations about Al Jazeera are not taken at face value," a spokesman for Al Jazeera said.
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