The rights organization said it obtained satellite images that indicated parts of Meiktila had been severely damaged. Myanmar imposed a state of emergency over central cities in March following fighting between Buddhist and Muslim communities.
Human Rights Watch said at least 40 people died in the latest violence, which it said was similar to fighting last year in Rakhine.
"The government should investigate responsibility for the violence in Meiktila and the failure of the police to stop wanton killings and the burning of entire neighborhoods," Asia Director for Human Rights Watch Brad Adams said from Bangkok.
Myanmar earned praise for political reforms that began in 2010. Human rights groups said reforms are in jeopardy given Myanmar's national security concerns.
Muslim leaders told The Irrawaddy, a Thai newspaper covering Myanmar, that few reports of violence have surfaced since last week. A member of the Meiktila police force told the newspaper on condition of anonymity there were no ultra-nationalists arrested in connection with the violence.
"We don't care about the suspects' religion," the police officer said. "But no monks have been detained."