But the Supreme Administrative Court said on Sunday that there was no conclusive evidence that the candidates or their supporters had used religious slogans while campaigning, clearing the path for the Brotherhood's full complement of 19 candidates to run in Monday's elections.
The authorities have intensified their crackdown on the Brotherhood, Egypt's strongest opposition group despite a 53-year-old state ban, before the Shura council elections.
Safwat al-Sherif, speaker of the Shura Council, has warned the Muslim Brotherhood that it was ready to crack down on groups that "defy the constitution and the law".
On Sunday, the group staged a sit-in protest after one of its members was beaten-up, allegedly at the hands of Egyptian police.
Egyptian authorities have arrested 22 supporters of the Muslim Brotherhood candidates in five provinces, Al Jazeera's correspondent in Cairo reported on Sunday.
The Brotherhood says more than 760 of its members were in detention, including 600 who were picked up after the beginning of the electoral campaign last month.
Forty members face a military trial on charges of money-laundering and financing a banned organisation.
The human rights group Amnesty International described the wave of arrests as a "serious violation" of freedom of expression.
The Brotherhood, which operates openly, fields members in general elections running as independent candidates to bypass the state ban.
It won nearly a fifth of the seats in the influential lower house of parliament in 2005.
The Shura council has a consultative role. Of its 264 seats, 132 are renewed every three years.
Of the 665 candidates in the running, 88 are elected and 44 are appointed directly by Hosni Mubarak, the president, who has ruled Egypt for more than a quarter of a century.
A second round of elections will be held on June 18.