Five people were killed near Egypt's Defence Ministry on Wednesday when armed "thugs" attacked Islamist protesters demanding an end to military rule after their candidate was barred from this month's presidential election.

The state news agency Mena said thugs, some of them with guns, had assaulted hundreds of mainly Salafi protesters, many of whom have been camped near the ministry for six days.

The Health Ministry said more than 100 people had been wounded, in addition to the five deaths, in the dawn fighting with sticks, stones, batons and bullets. Low-level clashes continued hours after the initial attack.

The violence casts a shadow over the presidential election due to begin on May 23 and 24, with a run-off in June, and highlights the fragility of Egypt's transition to democracy which has been punctuated by violence and political bickering.

Many of the demonstrators were supporters of an ultraorthodox Salafi sheikh who was disqualified from the presidential election, drawing accusations that the ruling military council was trying to dictate the result in advance.

There had been some scuffles near the Defence Ministry in recent days but protests had been broadly peaceful.

Residents gathered around a police station in the vicinity after the clashes, demanding that police disperse the protesters, whom they also accused of being thugs. Protesters often accuse state security of paying or encouraging thugs to quash peaceful demonstrations.

The army, which has pledged to hand over to civilian rule after the presidential election, has faced mounting criticism of its handling of the political transition a popular uprising overthrew President Hosni Mubarak in February 2011.

Nevertheless, many Egyptians suspect the generals will seek a strong influence even after the new president assumes power.     

Liberal pro-democracy groups, which were also involved in the protests demanding that the army return immediately to the barracks, condemned the attack at the Defence Ministry.

The April 6 Youth Movement decried the "massacres" and demanded the army be held to account for its "crimes committed against the revolution and revolutionaries".

"These practices are a continuation of the cleansing and killing methods which the army council uses to suppress the revolution," April 6 said in a statement.   - Reuters