Subash Chandraboas, 32, editor of the Tamil monthly Nilam, was gunned down late Monday at his residence in Vavuniya, 260 kilometres (162 miles) north of here, the Free Media Movement (FMM) said.
Chandraboas also freelanced for other publications.
The FMM, which consists of journalists and rights activists, said it was "appalled by this killing.
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"Although the reason for killing him is not clear, the FMM fears that this could be another attack on journalists and media personnel working in north and east," where fighting is raging between the government and Tamil Tiger rebels, the statement said.
The report on the killing comes after an editor from a national daily said she received a death threat from Sri Lanka's defence secretary Gotabhaya Rajapakse, a charge denied by him.
Media organisations have described Sri Lanka as the most dangerous place on earth for journalists after Iraq, and rights groups say that critics of government policy are treated as traitors and enemies of