The anti-junta demonstrators are marching against the so-called Abbasieh massacre that killed 20 people and left dozens of others injured.
The clashes took place early Wednesday when unidentified armed men used rocks, clubs and firebombs to target hundreds of protesters who had been camping out near the ministry for days.
The clashes, the worst in the capital in weeks, prompted four presidential candidates to temporarily suspend their campaigns in protest at the brutal handling of the peaceful sit-in.
The candidates — Mohammed Mursi, Abdel Moneim Abul Fotouh, Khaled Ali and Hamdeen Sabbahi — announced they were temporarily suspending their campaigns over the killings.
Hours after the clashes, protesters in Alexandria staged a massive rally outside the city’s military command center, denouncing the military rule in the country.
Egypt has been grappling with post-revolution unrest for more than a year now. The protesters want an end to military rule and the transfer of power to a civilian government.
Egypt’s election is scheduled to be held on May 23-24, and a run-off will follow on June 16-17 if necessary.