Quintana said his office has heard reports of violent clashes between national security forces and members of the minority Muslim community in parts of Rakhine, a coastal state.
"I urge the government to clarify what has happened," he said in a statement Friday. "If deaths and injuries have occurred, the Myanmar government must, under international law, conduct a prompt, effective and impartial investigation and hold the perpetrators of any human rights violations to account."
Quintana said there were reports security officials and Muslims were killed and injured as a result of recent conflicts.
The envoy said the situation in Rakhine was one of the most serious threats to Myanmar's reform processes.
Myanmar, formerly known as Burma, received international praise for holding democratic elections in 2010. Internal conflicts among various ethnic communities calling for more autonomy and a poor human rights record are lingering concerns.
The Irrawaddy, a Thai newspaper monitoring Myanmar developments, reported Wednesday a national cease-fire conference was postponed because ethnic groups wanted more time to coordinate their positions.