Opposition and civil society groups have prized the existing requirement that judges supervise elections as one of the best ways to discourage the abuses which have marred voting in Egypt.
In the 2005 elections several judges risked their careers by speaking out against electoral practices that they witnessed.
The parliamentary committee is expected to approve the amendments this week.
The Egyptian government does not allow the Muslim Brotherhood to form a party but under the existing system it could field a presidential candidate as an independent if it wins enough seats in parliament and local councils.
Mohamed Habib, deputy leader of the Muslim Brotherhood, said the proposed amendments would be a step backwards, perpetuating the present government and enabling the ruling party to install Gamal Mubarak in place of his father, Hosni Mubarak, Egypt's current president.
"The aim is to marginalise our role in Egyptian political life," Habib told Reuters who gained first-hand access to the new amendments.
The authorities began a crackdown on the brotherhood in December and about 310 members remain in custody, most of them without formal charges.
The proposed changes could also clear the way for the government and ruling party to change the electoral system so that the Muslim Brotherhood cannot compete even for parliamentary seats, as they did with some success in 2005.
Brotherhood members standing as independents won about one fifth of the seats in the lower house of parliament in 2005.
Parliamentary elections now take place under a simple constituency system but some officials have said they would prefer a party-list system, which would make it more difficult for the Muslim Brotherhood to take part.
The constitutional court ruled in 1987 that the party-list system was unconstitutional.
Mohamed Kamal, of the National Democratic Party said in December that the party wanted the constitution to give authorities the flexibility in choosing the best voting system.
The proposed amendment says: "The law shall determine ... the rules for elections and referendums."
The amendments also stipulate that parliamentary elections must take place on a single day.
The last elections took place in three stages because Egypt does not have enough judges to supervise all polling stations simultaneously.