The protesters included supporters of the disqualified Salafist candidate Hazem Salah Abu Ismail, whose candidature was ruled out on grounds that his mother had been given an American citizenship.
Abu Ismail warned last night of "unknown reactions" of his backers to what they see as "injustice" over his exclusion from the presidential race.
His comments came shortly after thousands of protesters, mostly his supporters, marched at midnight to Egypt's Defence Ministry, chanting slogans against Field Marshal Hussein Tantawi.
"Down with the military council," shouted demonstrators, calling on the generals who took over from Mubarak step down.
There has been an increasing perception among the people in Egypt that the ruling military may try to get a loyalist elected as the next president.
The election commission announced the final list of 13 candidates for the presidential election on Thursday after disqualifying 10 candidates.
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While two top Islamist candidates were disqualified, the candidature of Ahmed Shafiq, who served as prime minister in the deposed Mubarak regime during last year's uprising, was upheld.
Abu Ismail's supporters have staged a sit-in in Tahrir Square for more than a week now, protesting the Elections Commission's decision to disqualify him from the race after proving that his late mother had obtained an American nationality.
The protesters have demanded the dissolution of the elections commission.
The military police blocked the roads to the Defence Ministry but the protesters, estimated to be around 2,000, stayed overnight near the ministry, according to Al-Masry Al-Youm.
In a poetic post on Facebook, Abu Ismail wrote: "People feel that injustice blocks the road against them. This makes them leave their homes and beds and respond to the calls to break the chains".
Before his disqualification, Abu Ismail had emerged as one of the most popular presidential candidates. His simplistic rhetoric over following the Sharia and defending citizens' dignity attracted much support.
This month an opinion poll by Al-Ahram Center for Political and Strategic Studies showed that before his exclusion Abu Ismail had topped the presidential race with 26 per cent of votes, while Hosni Mubarak's spy chief Omar Suleiman, also since excluded, garnered 21 per cent of the votes. PTI RAG