Journalists and media workers told Al Jazeera they now lived in fear following the return of Rajapaksa to the political scene.
Several journalists with Sri Lanka's public media company said they "are thinking of quitting their jobs because of increased government censorship".
"We have been taken hostage," a journalist at Lakehouse told the news agency.
"Everything we write has to be approved by government supporters."
Tamil journalists across the North-East have also reported heightened fear following Rajapaksa's appointment.
A report by Together Against Genocide found that since the beginning of the reign of the United People’s Freedom Alliance coalition government in 2004, at least 48 journalists or media workers were killed on the island, making it one of the most dangerous places in the world for reporters.
In an interview just this week the former defence secretary, Gotabhaya Rajapaksa flatly denied that Tamil journalists were killed by the regime.
"Not a single Tamil politician or journalist was murdered during that period in Colombo or Batticaloa," Gotabhaya said.
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Recent weeks have seen increasing harassment and intimidation of journalists, particularly Tamil ones.