The reporters planned to attend a media conference by Lieutenant General Walit Rojjanapakdee, who heads the Army's region that covers Phuket.
Phuketwan journalists Alan Morison and Chutima Sidasathian are being sued by the Royal Thai Navy, using Thailand's criminal defamation and Computer Crimes Act laws.
The suit is over a paragraph from the Reuters news agency that was republished word-for-word in Phuketwan.
No charges have been laid against Reuters or any of the other organisations around the world that reproduced the same Reuters paragraph, among them Thaipost, T-News, kapook.com, manager.co.th and Sanook.com.
''We were shocked at being turned away at the Royal Thai Navy base today,'' said Morison, the editor of Phuketwan. ''This means that the Navy wants to stop Phuketwan doing its job of reporting all events of significance.''
The Royal Thai Navy's pursuit of Phuketwan was noted in the US State Department's Trafficking in Persons report earlier this year. The report downgraded Thailand to Tier 3, the lowest level.
After Phuketwan was sued by the Royal Thai Navy, a series of reports by Reuters on the Rohingya boatpeople - including the controversial paragraph - won the Pulitzer prize, one of journalism's highest honors.
The Reuters reports were also quoted in the US State Department's Trafficking in Persons report.
''What's happened is sad for Thailand, sad for Phuketwan and sad for the Royal Thai Navy,'' Morison said today, after being turned away.
''The Navy could have made one telephone call to Reuters or Phuketwan back in July last year and prevented this disaster.
''Instead, a few people within the Navy are choosing to try to shut down Phuketwan using Thailand's draconian laws.
''In doing so, they are bringing the military government of Thailand into disrepute.''
Morison and Khun Chutima have won international awards for covering the issue of the Rohingya, a Muslim minority who are forced to put to sea from neighboring Burma in large numbers because of ethnic cleansing by their Burmese neighbors in Rakhine state.
How thousands of them reappear in secret jungle camps run by human traffickers in southern Thailand, where they are abused and where deaths are common, has yet to be explained.
''We have the greatest respect for the Royal Thai Navy,'' Morison said today. ''However, we also have no intention of ending our coverage of the Rohingya issue.
''If the one or two people inside the Navy with a grievance against us wish to silence us, they will have to kill us.''
The Navy case against Phuketwan began to proceed in December, long before the military takeover of Thailand on May 22. The case resumes in Phuket Provincial Court on March 18 next year.
Because the case has not been stopped by the military government, it could be referred to again in next year's Trafficking in Persons report for 2014.
Morison, an Australian, has had his passport confiscated and cannot leave Thailand.
Phuketwan is likely to be forced to close in February, before the trial of the two journalists resumes, because Morison will be unable to renew his work permit.
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