The editor of Colombo's Daily Mirror, Champika Liyanaarachchi, said defence secretary Gotabhaya Rajapakse, the younger brother of President Mahinda Rajapakse, issued the threat in a telephone conversation Tuesday.
Liyanaarachchi said the president himself telephoned her later Tuesday to inquire into the threat.
"The president said he will look into it," Liyanaarachchi said. "There is no way of dismissing the threat.
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Media organisations have described Sri Lanka, where the government is fighting a bitter war against Tamil Tiger separatist rebels, as the most dangerous place on earth for journalists after Iraq.
Rights groups say that critics of government policy are treated as traitors and enemies of the state.
Although there is no formal censorship imposed, Sri Lankan authorities prevent journalists from travelling to areas held by the rebels, who are waging a separatist conflict that has killed more than 60,000 people since 1972.
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The Free Media Movement (FMM), which co