The journalists were "severely beaten" while covering the vote in Kawempe North, a district of the capital, Kampala, on March 13 by members of the army and an anti-terrorist agency, RSF said.
"They made us take off our shirts to cover our eyes, told us to lie down and hit us with sticks and the top of their guns," Abubaker Lubowa, a photojournalist for the Daily Monitor newspaper, told RSF.
Some journalists said their equipment was confiscated and later destroyed, while others recounted being held incommunicado for hours in an army van.
"They told us to lie down in the van, then pretend to sleep, to snore. They forced us to count to 15 and hit us at each number. The windows were covered. It was very hot," said Raymond Tamale, of NTV Uganda.
RSF Sub-Saharan Africa director Sadibou Marong called for a full investigation, saying the "extreme violence shown by the forces of law and order towards clearly identified journalists" was "unacceptable".
With Uganda set to hold a presidential election in 2026, RSF said it was "vital that journalists are able to work in complete safety".
Uganda ranks 128th out of 180 in RSF's World Press Freedom Index.
Journalists there face physical violence, restricted freedoms and legal constraints.
The candidate for President Yoweri Museveni lost the Kawempe North by-election to the party of his rival, Robert Kyagulanyi, known as Bobi Wine.
Museveni and the army have said they will investigate the conduct of the vote.
Army spokesman Chris Magezi said the violence was the result of a "misunderstanding and miscoordination" and that "the journalists must have been mixed up with violent supporters".
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