The think-tank, Sudd Institute, says lack of space for government critics has made the country more insecure.
The research group says those who find no room to exercise their constitutional right to question their government are forced to choose unconstitutional means, including violence and armed rebellion.
In a new report authored by co-founder, Prof Jok Madut Jok, the Sudd Institute says the government has taken major decisions of peace and war, all in the view of national pride and protecting the national sovereignty.
Mr Jok says the decisions are well-intended at the higher policy level, but are translated into bad actions by some individuals.
He says other individuals use state authority to settle their own conflicts with people they don’t like, and the blame goes to the government.
The report says it would help the image of the security agencies if they go after those individuals who translate policies into bad actions, with the view of punishing them.