Stephen Kwikiriza was found on Sunday evening dumped on a roadside in Kyenjojo, about five hours' drive west of the capital Kampala, said Samuel Okulony, director of the Environment Governance Institute.
The activist said he was beaten by army officers, Okulony said in a message to AFP, adding that he was being treated in a Kampala hospital.
"He is alive, is now safe, and is reconnecting with family. His condition is not good after having suffered severe beatings, mistreatment and abuse throughout the week."
A senior military officer on Monday confirmed Kwikiriza's detention.
"He was taken into custody for questioning regarding his illegal activities including mobilising fellow activists to oppose the oil pipeline," the officer told AFP on condition of anonymity, adding that he was released after interrogation.
"I have not been made aware of him being beaten during interrogation, it's a matter that can be investigated and verified."
- 'Escalation of repression' -
Okulony lauded "international pressure" for the release of Kwikiriza.
Global rights groups had raised concerns about Kwikiriza's fate after he went missing on Tuesday.
The International Federation for Human Rights (FIDH) described it as a "particularly worrying escalation of repression".
FIDH said 11 environmental activists "were kidnapped, arbitrarily arrested, detained or subjected to different forms of harassment by the Ugandan authorities between May 27 and June 5, 2024".
Human Rights Watch (HRW) had also voiced concern about Kwikiriza's disappearance.
"The Ugandan government needs to end its harassment of opponents of oil development in the country, such as the East African Crude Oil Pipeline Project," Myrto Tilianaki, senior environmental rights advocate at HRW, said in a statement.
TotalEnergies signed an agreement with the China National Offshore Oil Corporation (CNOOC) in 2022 to develop Ugandan oil fields and ship the crude via a 1,445-kilometre (900-mile) pipeline to Tanzania's Indian Ocean port of Tanga.
President Yoweri Museveni, who has ruled Uganda with an iron fist since 1986, has regularly praised the oil project as an economic boon for the impoverished landlocked country.
The first oil is expected to flow in 2025 -- almost two decades after the reserves were discovered in Lake Albert in northwestern Uganda.
Environmental groups say the project is having dire consequences for local communities and the environment in an area of rich biodiversity, and have accused TotalEnergies of greenwashing.
TotalEnergies in Uganda said in a statement it "does not tolerate any threats, intimidation, harassment or violence against those who peacefully and lawfully promote human rights in relation to our activities".
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