Quintana published his 22-page report on the human rights situation in Myanmar, more than four years after the Asian country earned international praise for ending a long period of military rule with general elections.
The envoy said in his report the military still has a "prevailing role" in most institutions in the country.
"State institutions in general remain unaccountable and the judiciary is not yet functioning as an independent branch of the state," his report stated. "Moreover, the rule of law cannot yet be said to exist in Myanmar."
Quintana said a change of mind-set was needed at all levels of the government in order to make room for civil society.
He added that a "critical step" in addressing national security would come through reaching cease-fires with the various ethnic minority groups fighting for more rights in the country.
Myanmar has struggled with ethnic violence from the restive states of Rakhine and Kachin. If left unaddressed, the envoy said, the entire political transition process could be spoiled.