Egypt's election committee said 98.1 per cent of voters have approved a new, military-backed constitution in the first vote since a coup toppled the country's president.

Egypt's High Election Commission said that 38.6 per cent of the country's more than 53 million eligible voters took part in the two-day poll. That is 20.5 million voters casting ballots.

This is the first vote since the military removed Egypt's first freely elected president, Mohammed Morsi, following massive protests in July. Officials view the vote as key in legitimising the country's military-backed interim government and its plan for parliamentary and presidential elections.

But Morsi's supporters and his outlawed Muslim Brotherhood group boycotted the vote and have alleged the results were forged. The Brotherhood has vowed to keep up their near-daily protests.

Judge Nabil Salib, who heads the commission, called the vote an "unrivalled success" and "an unprecedented turnout." However, a similar referendum in 2012 supported by Morsi's government saw a 32.9 per cent turnout.

While announcing the results, Mr Salib suggested voter participation would have been higher if it were not for the vote coinciding with university midterm exams that kept students, and younger voters, away.

Activists and monitoring groups have raised serious concerns over the atmosphere in which voting took place, with US-based Democracy International saying that "arrests and detention of dissenting voices" took place ahead of the poll.

"A democratic transition should be characterised by an expansion of freedoms, but Egyptians have seen substantial restrictions on the exercise of their democratic rights," said Eric Bjornlund, Democracy International's president and head of the observation mission in Egypt.

In the lead-up to the vote, police arrested those campaigning for a "no" vote on the referendum, leaving little room for arguing against the document.

Yesterday, supporters of Morsi took to the streets to denounce the draft charter. Some protests turned violent. Four people were killed in the ensuing clashes, Egypt's Health Ministry said. It said 15 people were injured nationwide.