None of its 49 candidates involved in the third and final phase of voting won outright, compared with 13 in the second stage, although 35 will be contesting run-offs next Wednesday.
Issam al-Aryan, the Brotherhood spokesman, said: "The fact that no Muslim Brother won in the first round is the result of the fact that voters were prevented from voting and that the Ministry of Justice assigns notoriously dubious judges to the tallying centres."
According to partial and unofficial results on Friday, 10 ruling National Democratic Party candidates won a majority of the vote at their first attempt, and one from the liberal Wafd party.
On the fifth day of voting in Egypt's month-long elections, police sealed off polling stations, preventing voters from casting their ballots, mainly in Nile Delta Islamist strongholds.
Teargas was used by the security forces to repel demonstrators, but in some areas voters squeezed into polling stations.
"We are concerned about the violence that has surrounded recent phases of the Egyptian electoral process"
US State Department spokesman Sean McCormack
The Muslim Brotherhood had hoped that its 49 third-phase candidates would be enough to take its seat tally past 100, having secured 76 seats in the first two phases.
Al-Aryan said: "The NDP is using all possible means to prevent the Muslim Brotherhood from obtaining 100 seats in parliament.
"Cheating is their only resort since despite attempts to hamper polling, we have won many votes."
The dominance of President Hosni Mubarak's National Democratic party is not at risk; but it had to secure 90 seats in the final phase to retain the two-thirds majority needed to change the constitution and pass emergency laws.
Washington, which has made Egypt one of the kingpins of its policy of democratisation in the Middle East, voiced its concern over the violence.
The elections on Thursday were
marred by violence
Sean McCormack, the US State Department spokesman, said: "We are concerned about the violence that has surrounded recent phases of the Egyptian electoral process.
"But these elections are, overall, an important step on Egypt's path toward democratic reform."
Campaigning under the slogan "Islam is the solution", the Muslim Brotherhood movement founded in 1928 made large gains in the first two phases and demonstrated its popular support base.
Its surprise showing in the elections will boost its case for legalisation as a political party, an option Mubarak's government and Washington have consistently ruled out.