Egypt's newly elected president must order an end to military trials of civilians to bring the country in line with international law, campaign group Human Rights Watch said in a report on Sunday.
Egypt's army generals handed over power to the Muslim Brotherhood's Mohamed Mursi last month but are likely to keep parts of the state apparatus under their control, limiting the president's influence over the military.
At least 12,000 civilians, including children, have been tried by military courts behind closed doors since the uprising in January last year that ousted former President Hosni Mubarak - more than in Mubarak's three-decade rule, according to rights groups.
"Now is the time for President Mursi to carry out his promises to end military encroachment on civilian decision-making and uphold human rights by ending military trials of civilians once and for all," Sarah Leah Whitson, Middle East and North Africa director at Human Rights Watch (HRW), said in a statement.
If there was evidence that a civilian had committed a crime, they should be tried by a civilian court, she said.
Mursi formed a panel this month headed by a judge to investigate cases of civilians convicted by military courts.
The committee said 2,165 civilians remained imprisoned after being sentenced, according to the military, and recommended they be pardoned by the president.
"International law is crystal clear on this - no civilian, regardless of the crime, should be tried by a military court. It doesn't take a committee to confirm that," Whitson said.
HRW said the most recent figures issued by the military judiciary on the number of civilians tried by military courts did not appear to be accurate as they had not been updated since last year despite ongoing arrests and trials of civilians.
The group's report cited the case of three political activists who were arrested on Thursday and detained for four days after taking part in a peaceful protest near the home of the head of the military police. The activists are members of the Egyptian Social Democratic Party, it said.
It also cited the sentencing on July 9 of eight protesters - one aged 16 - by a Suez military court, for using fireworks that could be considered explosives at a protest. The sentences ranged from six months to three years, the group said.
"The Muslim Brotherhood's position on ending military trials of civilians is already in doubt after their failure to any way limit the military's right to continue referring civilians to military courts," Whitson said.
"(Mursi's) committee will not have the mandate to look at these more recent cases because it will only look at convictions up until June 30, 2012," the report said, referring to the date when the army officially handed over power.
The report said a presidential pardon was the only way an unfair decision by a military court could be overturned.