The rights group, one of the largest in the DRC, said Chebeya had been due to meet the police chief the night before his death.
The group also said he appeared to have been strangled. The driver of the car has not been found since contact was lost with Chebeya on Tuesday evening.
Several police officers, including Daniel Mukalay, head of the police special service, were arrested on Saturday in connection to the death.
More than 50 human rights groups, including Amnesty International and Human Rights Watch, have demanded an independent enquiry into the killing in an open letter to Joseph Kabila, the Congolese president.
Erwin van der Borght from Amnesty International said Chebeya had been arrested and threatened in the past.
"Threats and intimidation [are] unfortunately part of the working environment in which [rights activists in the DRC] have to operate," he told Al Jazeera.
"We certainly believe the Congolese authorities contribute to that hostile environment, either by the security forces' attitude towards human rights activists by regularly arresting them and intimidating them, but also by the statements made by government officials towards the work of human rights organisations."