A total of 10 candidates have been barred from standing in the presidential poll in May.
Hundreds of supporters of hardline Islamist candidate Hazem Abu Ismail had been protesting outside the defence ministry.
They said they were attacked by thugs they believe were government agents.
Other reports have described the attackers as local people angry at the protest. But the BBC's Jon Leyne, in Cairo, says that the use of plain-clothed thugs is certainly a tactic that has been used by the Egyptian authorities in the past.
Our correspondent says that the demonstrators have called for reinforcements to come and protect them and there is a danger of more clashes.
A first round of elections is due in May, more than a year after former President Hosni Mubarak was forced to step down after an 18-day popular uprising.
Ultraconservative Mr Abu Ismail was banned from standing for president because his late mother had US citizenship.
Egypt is still governed by a military council, although parliamentary elections have taken place in the meantime.