The OMCT, a Geneva-based NGO, listed "serious human rights violations" during protests on Thursday against a move by Chad's military ruler to extend his grip on power for two more years.
"Bodies of slain protesters were recovered from the Chari River in N'Djamena over the weekend," the OMCT statement said, noting school classrooms had been turned into prisons at the Abena Communal high school in the capital.
"Young people were reportedly summarily executed there this morning (Monday)," the statement said, adding that hundreds had been arrested and some tortured.
The OMCT and three Chadian human rights organizations have taken up the case with United Nations special experts, requesting an immediate investigation.
Chad's opposition had called for peaceful protests last Thursday to mark the date when the military had promised to hand over power in the unstable Sahel country.
The transitional government has admitted 50 people died in the protests, including a dozen members of the security forces and blamed an "insurrection."
Junta head Mahamat Idriss Deby — a 38-year-old five-star general who has held power since his iron-fisted father was killed in an operation against rebels in April 2021 — said in a televised speech on Monday a "meticulously prepared insurrection" had taken place with the "support of foreign powers," which he did not name.
There was a "clear desire to trigger a civil war" he said, claiming opposition and rebel groups had "recruited and used terrorist and paramilitary groups to carry out gratuitous mass killings."
But medical sources and NGOs spoke of dozens shot by live fire from the security forces.
The watchdog reported at least 80 deaths in a provisional casualty toll in N'Djamena and four southern towns: Moundou, Doba, Koumra and Bebedjia.
The U.N. said it "deplored the lethal use of force" and called for an investigation into reports of human rights violations.
The African Union and the European Union have also condemned the repression of the protests.
