The condemnation came a day after authorities formally charged J.S. Tissanayagam with inciting racial hatred and bringing disrepute to the government.
The journalist, who has been in detention since being arrested in March, is also accused of supporting terrorism by collecting money from donors to publish his website in the country racked by deadly civil war.
The New York-based Committee to Protect Journalists (CPJ) said it condemned the Colombo High Court's indictment of Tissanayagam.
The journalist was brought to court to hear the charges and a hearing was slated for next month. He has denied all the accusations.
"We condemn J.S. Tissanayagam’s long detention and harsh charges for publishing a magazine which should not constitute an offence," said Bob Dietz, CPJ Asia Program Coordinator.
"This is the latest step by the Sri Lankan government to intimidate journalists who write about security issues," he said.
Tens of thousands of people have died since the the Liber