The report, A High Price to Pay: The Detention of Poor Patients in Hospitals, was released by Human Rights Watch and the Burundi Association for the Protection of Human Rights and Detained Persons.
Human Rights Watch said: "Patients who could not pay their bills were kept under guard and prohibited from leaving the hospital grounds often for weeks or months, but in one case a year."
Healthcare for mothers and children under five is free in the tiny central African country whose shattered economy is emerging from more than a decade of ethnic conflict.
But hospital fees are beyond the reach of a majority of its seven million people, most of whom live on less then $1 a day.
The report quotes several patients, though does not give their full names to protect their anonymity.
Felix M, a 12-year-old boy held for more than a year at Prince Regent Charles hospital in Bujumbura after a car accident, said: "My family cannot pay the bill. I have been told that I cannot leave unless the bill is paid, I cannot go past the exit."
Another patient, 18-year-old Christine K, was detained at the Louis Rwagasore Clinic, also in Bujumbura.
She said: "Life is difficult, I don't have permission to leave with my baby, we are often hungry here. I cannot stand this situation any more."
The report said that in some cases hospital authorities refused further medical care to those who could not pay their bills and forced them to vacate their beds for wealthier incoming patients.
It urged the government to order the release of all hospital detainees and to improve access to healthcare for the poor.