"The timing of the law is very worrying, when we have around 300 people detained after Abbassiya," said Heba Morayef of Human Rights Watch.
She was referring to Cairo's Abbasiya district near the defence ministry where deadly clashes between anti-military protesters and troops erupted this seek. The army arrested hundreds after the skirmishes Wednesday and Friday.
Morayef told AFP that the amendments "limit the powers of the president to refer civilians to military trials but they retain the right of the military to refer civilians to military trial."
"Parliament has failed to live up to one of the main demands of the revolution which is to end the military trials of civilians," she said.
"Parliament is not listening to the street."
The amendment, read in parliament, indicates that Article 6 which previously allowed the president to refer civilians to military courts has been scrapped.
But Article 48 allowing the army to refer civilians to military courts remained unchanged.
The Supreme Council of the Armed Forces, which has been ruling Egypt since president Hosni Mubarak was ousted from power last year, must ratify the amendments in order for them to be effective.
"It is a very worrying development, particularly that parliament is dominated by people who have suffered from military trials. If they fail to push for reforms on this front, there is no reason for optimism on other issues," said Morayef.
Egyptian human rights lawyer Adel Ramadan told AFP that the changes were only "cosmetic."
"The amendment is cosmetic. Nothing has changed," he said, adding that civilians could still be tried by military courts.