Uganda's security forces routinely torture suspects, the Human Rights Commission says in its annual report.
Some security agencies are trained in torture, the report says
The report says torture is "indispensable" in the operations of some security agencies.
Beatings, blind-folding and death threats are some of the methods used to extract confessions by the Crack Crime Unit, the Monitor newspaper reports.
In March, Human Rights Watch accused the authorities of using torture as a method of suppressing opposition.
The New York-based organisation said the safe houses provide Ugandan security and military forces with the opportunity for unseen torture and interrogation of suspects.
These reports were denied at the time by presidential advisor John Nagenda.
He said all such reports were investigated and taken before the courts and described the report as "rubbish born of a fevered imagination"
Nathan Byamukama of the Uganda Human Rights Commission says there has been progress with dismantling them.
"Although we are still getting reports of people who come and say there were tortured in safe houses," he told the BBC's Focus on Africa programme.
"Our report indicates that torture is the second highest violated human right," he said, with deprivation of personal liberty - those arrested but not charged within 48 hours - topping the list.
"[Torture] is either presented as part of training, or a learned practice," the report says.
"We need to explain to all officials that actually torture is not acceptable under any circumstances and the government has already ratified the convention against torture," Mr Byamukama said.
According to Mr Byamukama, freedom of speech in the country has improved because of the proliferation of private FM radio stations.
But violations of homosexual rights are still to be investigated, he said.
Earlier this month, a radio station was forced to pay a fine for hosting homosexuals in a live talk show, as homosexuality is illegal in Uganda.
He called for the constitution to be amended to take into account inconsistencies with international human rights legislation.