The EU has criticised Egypt for the way it deals with protests and dissent.
The opposition reported dozens of arrests during Thursday's protests
The union expressed concern over the " disproportionate" use of force against protesters in Cairo last week.
The security forces beat activists and assaulted and detained journalists during protests in support of judges who face disciplinary action.
The EU also urged the government to repeal its long-established emergency laws and, until then, to restrict their application to fighting terrorism.
Washington has already condemned the security forces' action.
Last week's protests in central Cairo were in support of Hesham Bastawisi and Mahmoud Mekki, two senior judges who face dismissal for criticising last year's presidential election as fraudulent.
The case has put the judges at the centre of a campaign for political reform.
A statement from officials in Austria, which holds the EU's rotating presidency, said: "The European Union calls on the Egyptian government to allow civil society activists and other political forces to express themselves freely, to permit peaceful demonstrations and freedom of assembly and to maintain public order by transparent and proportionate legal procedure."
The statement also expressed concern "that many persons taking part in these demonstrations have been arrested and are being held in custody".
The EU statement adds that the union hopes Egypt would not again extend the emergency laws beyond 2008, and notes that President Hosni Mubarak had promised in 2005 to repeal the measures and ensure they were used only to combat terrorism, not target the political opposition.
Egypt renewed the emergency laws in April for another two years. The laws have been in place since President Anwar Sadat was assassinated in 1981.