At least 10 activsts have been seriously injured in confrontations with the police.
The Brotherhood says more than 100 members have been arrested.
The government postponed the 2006 local elections for two years, after the group unexpectedly won 88 seats in the 454-member parliament in 2005 elections.
Prevented from registering
Since registration started on March 4, thousands of the Muslim Brotherhood's candidates have been prevented from registering for the local council elections, set for April 8.
Later the group won law suits reversing these decisions, but the government has refused to implement the verdicts.
The Brotherhood, the most powerful opposition group in Egypt, has been banned in Egypt since 1954 but its members have won parliamentary seats by running as independents in elections.
Subsequently, the Egyptian authorities have launched a major crackdown on the Brotherhood, putting more than 800 of the group's members and potential candidates in jail.
The arrests have drawn criticism from White House and several international human rights organisations.