"We have had, from our point of view, an attempted coup d'etat. The armed forces stopped this attempt," Prime Minister Patrice Trovoada said during a visit to Portugal.
"After the end of the operation, some hours afterwards, there were what we think were extrajudicial executions, the execution of people who were key witnesses," he said in an interview published Wednesday by the Portuguese agency LUSA.
"At the very least, there was a failure in command. People placed under the responsibility of the armed forces cannot die -- they are in detention," he said.
Authorities previously said four people were killed after military headquarters in the capital Sao Tome came under a gun attack on the night of November 24.
Photos and videos have been circulating online, purportedly showing men in military uniform brutally interrogating and torturing three detainees. AFP has not been able to independently verify the images.
On December 1, the government ordered an investigation into allegations that soldiers committed "cruel, degrading and inhumane acts."
Armed forces chief Olinto Paquete also announced he was resigning, saying he could not "accept such atrocities and acts of treason that harm the homeland."
The turbulent episode has rocked the reputation of Sao Tome, a nation off the coast of central West Africa, for stability since it gained independence in 1975.