Wadah Khanfar, director-general of Al Jazeera, said in a statement issued on Friday: "Any code of ethics or governance for journalistic practices should emerge, and be governed, from within the profession and not be imposed externally by political institutions.
"Al Jazeera considers the adoption of the charter ... a risk to the freedom of expression in the Arab world."
All members of the 22-member Arab League had voted in favour of the document, with only Qatar and Lebanon opposing.
Qatar said it was "still studying the document" and that it did not "currently want to adopt" it for legal rather than political reasons.
Tuesday's meeting was called at the request of Egypt, which hosts the Arab League and serves as a base for several Arab satellite channels.
"The region has seen the recent emergence of many media institutions and every attempt should be made ... to encourage their independence and freedom"
Wadah Khanfar, director-general of Al Jazeera
Anas al-Fiqi, the Egyptian information minister, said his country would be the first to implement the charter.
"Some satellite channels have strayed from the correct path," he said.
But in his statement, Khanfar says: "Some of the language contained within the charter is ambiguous and could be interpreted to actively hinder independent reporting from the region."
Any violation of professional ethics should be tackled through independent legal processes, he said.
"The region has seen the recent emergence of many media institutions and every attempt should be made not to hamper, but to facilitate, an environment to encourage their independence and freedom," Khanfar said.
Al Jazeera has faced reporting bans in several Arab countries including Kuwait and Saudi Arabia over the past decade.
Iraq also banned Al Jazeera Arabic from reporting in Iraq three years ago - accusing it of fomenting sectarianism - but Al Jazeera English has a presence in Baghdad.
The Cairo charter stipulates that channels should "refrain from broadcasting anything which calls into question God, the monotheistic religions, the prophets, sects or symbols of the various religious communities".
It says broadcasters should avoid "erotic or obscene material" or programmes that "encourage smoking or the consumption of alcohol", the latter prohibited by Islam.
They should also "protect Arab identity from the harmful effects of globalisation".
Speaking to Al Jazeera, Agnes Callamard from Article 19, a press freedom organisation, said: "This is turning into the next stage of censorship which is to try to prevent millions of people in the region to access information.
"The guidelines that have been put forward are so overbroad and over-reaching, they are just really trying to impose a curtain of censorship over the provision of information and simple provision of