Home minister Asaduzzaman Khan rejects the allegations, says the detentions were lawful and accuses New York-based Human Rights Watch of spreading "propaganda".
Bangladesh has secretly detained hundreds of people including scores of opposition activists, many of whom have later been killed, a rights group said Thursday.
The Human Rights Watch report, released days after the alleged abduction of a high-profile government critic, said security agencies were removing people with "no regard" for the rule of law.
Hundreds of people have been detained and held in secret locations since 2013, including at least 90 last year, it said.
"Bangladesh security forces appear to have a free hand in detaining people, deciding on their guilt or innocence, and determining their punishment, including whether they have the right to be alive," HRW's Asia director Brad Adams said.
"The disappearances are well-documented and reported, yet the government persists in this abhorrent practice with no regard for the rule of law," he said.
The New York-based group said in 2016 alone it documented 21 cases of detainees who were killed, and nine others whose whereabouts are unknown.
Among those missing is Sajedul Islam Sumon, 37, a Dhaka neighbourhood chief of the main opposition Bangladesh Nationalist Party (BNP).
Sumon's sister Sanjida Islam said officers from the country's elite Rapid Action Battalion (RAB) detained her brother and five other BNP activists on December 4, 2013. This was one month before a controversial 2014 general election which the BNP boycotted.
"Some 20 construction workers who were on the site told us RAB officers picked them up and led them away in a RAB van. They were never returned," Islam said.
"For the last three years and eight months we've knocked on doors, gone to every agency's office and met the home minister to know my brother's whereabouts," she said.
Islam said the family was hopeful her brother, a father of two, would be found.
Political tensions are rising in Bangladesh ahead of a national election due next year.
The BNP and its ultra-conservative ally Jamaat-e-Islami have said tens of thousands of their activists and supporters have been arrested in recent years.
Bangladesh home minister Asaduzzaman Khan, however, rejected the allegations, saying the detentions were lawful and accused HRW of spreading "propaganda".
"Since Bangladesh's inception they are trying to spread a negative propaganda which has no similarity with the reality," he told reporters.
The mothers of 22 of the missing activists have set up a group, Mayer's Daak (Mother's Call), to seek answers from the government on the cases.
Meanwhile, police have filed a kidnapping case over the disappearance of government critic Farhad Mazhar, who was found on a coach earlier this week after his wife reported him missing.
Abdul Baten, the joint commissioner of the detective police, quoted Mazhar as saying he had been blindfolded and taken away in a vehicle.