"The constitutional court ruled unconstitutional some articles of the parliamentary election law related to the direct vote system," state-run MENA news agency reported, referring to the third of seats elected on a first-past-the-post system.
The ruling, which could create a fresh political turmoil in the country, came after a lower court verdict said that the principle of equality was violated when parties fielded candidates for the third of seats set aside for independent candidates.
This might mean the entire parliamentary elections are to be repeated. Parliament is expected to be suspended until new elections are held for these seats.
The Egyptian Supreme Constitutional Court also rejected a law which would have barred the former Prime Minister in Hosni Mubarak's regime Ahmad Shafiq out of the Egyptian presidential race.
The ruling would allow Shafiq to contest the presidential runoff on Saturday and Sunday against Islamist Mohammed Morsi despite a legislation banning old regime figures from running for office.
The disenfranchisement law prohibits high ranking officials of the former regime from running for high level official posts.
The rejection of the law was received by angry protesters and angry Muslim Brotherhood members who had surrounded he premises of the High Commission for Presidential Elections chanting against the commission as it refused to give them the database of voters.
The Muslim Brotherhood is also calling their candidate Mursi the rightful president.