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 Liberation Tigers of Tamil Eelam (LTTE) launched a separatist campaign in 1972 to carve out a homeland for minority Tamils in the majority Sinhalese island's north and east.
Sri Lanka's Free Media Movement also denounced the use of the Prevention of Terrorism Act against Tissanayagam, an ethnic Tamil, for an article he wrote in 2006.Under the act, there is no upper limit on prison terms for those found guilty. The state can also confiscate the property of those convicted.
Reporters Without Borders has also condemned the journalist's incarceration.
Media rights activists have described Sri Lanka as one of the most dangerous places in the world for journalists due to a worsening climate of violence and unofficial censorship.
Killings and attacks against journalists remain unsolved, leading to fears that media freedom is being violently suppressed through threats, abductions and attacks, a team of media activists said last year.
Since August 2005, 12 media workers have been killed in Sri Lanka, regarded as the second most dangerous place for journalists after Iraq.
Eleven of them died in government-controlled areas and no one has been brought to justice in connection with the deaths.