"RSF expresses its deep concern after blogger Yassine Ayari was sentenced in absentia", it said in a statement, calling for his case to be transferred to a civilian court that would "guarantee impartiality and independence".
Last November 18, the military tribunal sentenced Ayari to three years on charges of having "defamed army officers and senior defence ministry officials".
Ayari, 33, returned to Tunisia from abroad on December 25 and was arrested on arrival, his lawyer said.
He had accused the military officials of financial abuse, the military prosecutor said in a statement.
The blogger had been unaware of the verdict against him for "undermining" the army, his lawyer Sami Ben Amor said, adding that the verdict was "very harsh".
On Friday, RSF's Lucie Morillon called Ayari's conviction unacceptable.
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"The conviction of a civilian blogger by a military court is unacceptable for a country like Tunisia, undermining its process of consolidating democracy," she said.
"(The charge of) attacking the honour of the army, the main accusation against Yassine Ayari in the military court, represents a dangerous and draconian legal instrument" against freedom of expression, one of the main achievements of the 2011 revolution, Morillon added.
Ayari, who has posted on Facebook that he stands by every word he has written, has appealed the charges against him and a new hearing in the case has been set for January 6, Ben Amor said.
The blogger was also an activist during the regime of now ousted dictator Zine El Abidine Ben Ali.
Ayari's father, an army colonel, was killed in a clash with jihadists in May 2011 at Rouhia in the northwest.
In recent months he has been highly critical of Nidaa Tounes, which won October's landmark general election, and of the party's leader Beji Caid Essebsi who became president last month.
Essebsi is a veteran politician who served under previous Tunisian regimes, including in the government of Ben Ali who was ousted in the 2011 uprising that sparked the Arab Spring.