Gotabhaya Rajapaksa is the brother of president Mahinda Rajapaksa.
The comments came after journalists staged a public protest against last week's brutal assault on a senior editor of The Nation newspaper whose writings had been critical of the military.
It was the latest in a string of attacks on the media.
The letter said the media groups were "extremely disappointed and very concerned" to learn that Rajapaksa had summoned two journalists in a state newspaper who were leading the Sri Lanka Working Journalists Association to complain about their participation in the public demonstration.
It said Rajapaksa had made "thinly veiled threats" against the two journalists should they continue to defence the ri