Mr Thompson's concerns came as a reaction to the Metropolitan Police's attempt to attain a production order for the Guardian to reveal its sources in its reporting of the News of the World phone-hacking scandal.
Although Scotland Yard dropped its action, Mr Thompson described the move as part of a growing trend of the police to oblige journalists to disclose information about sources as well as footage of incidents like this summer's riots.
He went on to say:
"It would be easy to respond to the completely unacceptable actions of some journalists at the News of the World by adopting such a draconian approach that even the best journalism is constrained."
Mr Thompson warned, that creating a single media regulator, could potentially limit press freedom and that should the situation arise, the state "would have a single lever with which to do so."
"Plurality of regulation is a good thing. One of the safeguards that broadcasters in the UK have is the presence of a far less regulated press which can draw attention to any attempt by the authorities or anyone else to misuse their powers when it comes to broadcasting."
Commenting on the phone-hacking scandal which led to the resignation of News International chief executive, Rebekah Brooks, Mr Thompson defended the actions of the Guardian, saying:
"I can think of no better example of a journalistic disclosure being in the public interest than the Milly Dowler story in the Guardian. That anyone in the Metropolitan police should ever have thought otherwise is not only incomprehensible but disturbing."