Egyptian activists and political figures on Thursday accused the military of a "soft coup" after the top court ruled the parliament illegal but kept an ex-prime minister in the presidential race.

They said a court decision that effectively voids the elected parliament and will probably mean legislative power reverts to the armed forces was a sign that the army was unwilling to cede the power it took after Egypt's 2011 uprising.

And they slammed the court's decision to keep Ahmed Shafiq, a former prime minister under ousted dictator Hosni Mubarak, in the race for president that goes to a second round on June 16 and 17.

"I'm disappointed beyond words," activist Ibrahim al-Houdaiby said.

"This is in many ways a soft military coup. Now we have the parliamentary power going back to the Supreme Council of the Armed Forces, they will have their presidential candidate, they have the arrest laws. So we are going back to square one."

The court's decision came a day after the justice ministry announced a decision allowing army personnel to arrest civilians, a power they lost with the lifting of the much-criticised decades-old state of emergency last month.

"Despite all the criticism of the parliament, it was the only elected body of the post-Mubarak era," noted activist Wael Khalil.

"SCAF was the one who put in place the law for the elections. That was nearly 10 months ago and now all of a sudden they discover that it's unconstitutional? Of course it's a political decision."

The court based its decision on what it said were illegal articles in the law governing parliamentary elections that reserved a third of seats for directly voted independents, or party members, and the rest for party lists.

Egypt's military decided on a complex electoral system in which voters cast ballots for party lists which made up two thirds of parliament and also for individual candidates for the remaining seats in the lower house.

The individual candidates were meant to be "independents," but members of political parties were subsequently allowed to run, giving the powerful Muslim Brotherhood's Freedom and Justice Party (FJP) an advantage.

Abdel Moneim Aboul Fotouh, a moderate Islamist who stood for president in the first round of the race, described the court's ruling as a "complete coup."

"Keeping the military candidate and overturning the elected parliament after granting the military police the right to arrest is a complete coup," he wrote on his Facebook page.

"Whoever thinks that the millions of youth will let it pass is deluding themselves."

Houdaiby said the Brotherhood bore some of the blame for the court's ruling.

"They have had a zillion chances to bring more people on board. Had they done that, this decision would have been impossible, because it reflects the balance of power," he said.

"If they had brought all their competitors on board, the consequences of this decision would have been too great."

Many activists expressed simple fatigue after the disappointing ruling, which comes on the heel of what they saw as a weak verdict against Mubarak and a first round presidential race that left them with the unpalatable choice between Shafiq and Muslim Brotherhood candidate Mohammed Mursi.

"Egypt just witnessed the smoothest military coup," wrote activist Hossam Bahgat on Twitter. "We'd be outraged if we weren't so exhausted."