The Egyptian Organisation for Human Rights (EOHR) also called for an investigation into police violence that resulted in the death of one protester.
EOHR's 35-page report listed the names of 498 Muslim Brotherhood members and supporters it said were detained after peaceful demonstrations in 10 Egyptian provinces in the first week of May.
It said more than 1800 demonstrators were detained.
The report, Muslim Brotherhood: Suspects Without a Crime, said the Interior Ministry should issue clear orders to security forces not to use violence to disperse protests. It cited the use of electric sticks, rubber-coated and live bullets, and said violators should stand trial.
Demonstrator's death investigated
The ministry's practices are "a dangerous indication" against the right to peacefully protest, the report said. The EOHR report cited witness accounts and the initial forensic report of the death of Tariq Ghannam, a 38-year-old demonstrator, in the Nile Delta town of Talkha on 6 May.
The Muslim Brotherhood has been
demanding political reform
The forensic report said Ghannam died from suffocation after inhaling tear gas, according to EOHR's report, which included a copy of the letter written by the doctor to the prosecution. A final forensic report is yet to be released, and the rights watchdog asked the Interior Ministry to bring to trial those responsible for Ghannam's death.
Witnesses told EOHR that Ghannam was chased into the mosque, outside of which the demonstration was held, after he suffered from tear gas inhalation.
"What I saw is that it (tear gas bomb) landed in front of (Ghannam), and when he inhaled too much smoke, he ran toward the mosque, and the soldiers ran after him and hit him and that was inside the mosque," a witness told an EOHR mission.
The Muslim Brotherhood, banned since 1954, long refrained from provoking the government, but has engaged in protests since March demanding political reform.
Leaders of the group say about 2500 Brotherhood members were detained after protests earlier this month in 16 Egyptian cities. Police have said more than 800 were arrested.
Egypt's largest Islamist group, the Brotherhood was established in 1928 and advocates an Islamic government. It renounced violence in the 1970s.
Several hundred Brotherhood
members have been detained
Brotherhood supporters sit as independents in parliament, holding 15 seats that makes them the biggest opposition bloc.
EOHR's report also demanded the lifting of Egypt's emergency laws "which contradict reform claims." Local and international human rights groups have been calling for lifting emergency laws imposed by Egyptian President Hosni Mubarak in 1981 after the assassination of former President Anwar Sadat.
Critics say the laws, which give security forces broad powers - including great leeway in making arrests - are used to stifle opposition.
The government has never confirmed the number of political detainees or militant suspects and their relatives.
Opposition sources estimate them to be up to 20,000.