Official results on Sunday showed that the Islamist group has won a total of 76 seats so far, more than five times the number it held in the outgoing chamber.
About a third of parliament's 444 elected places have still to be decided.
The Brotherhood, which is banned but tolerated, is contesting only a third of the seats, not posing a challenge to control over parliament by the ruling National Democratic Party (NDP), which won 75 places in voting on Saturday, bringing its total to 195.
But the Brotherhood's wins have shown the weight of political Islam as the strongest opposition force in Egypt and caught the government and NDP off guard.
Curbs on Islamists
The authorities have curbed leeway given to the Islamists in the early stages of voting. Police restricted voting and detained 860 of the Brotherhood's activists on Saturday - the fourth of six days of legislative elections.
Riot police cordoned off polling stations in Brotherhood strongholds, either preventing anybody from voting or allowing only a trickle of people to cast ballots.
Brotherhood deputy leader
Muhammad Habib, the deputy leader of the Brotherhood, said: "The aim was to prevent voters from reaching the ballot boxes and to affect the result.
"But with perseverance the people and the Brotherhood were able to overcome the barriers."
The Brotherhood said its candidate in the oasis town of Fayoum south of Cairo had defeated Yusuf Wali, a high-ranking NDP official and former deputy prime minister.
A Brotherhood candidate also defeated Khalid Muhieldin, head of the opposition Tagammu Party and one of the last surviving leaders of the 1952 coup that overthrew the monarchy, the Brotherhood said.
Secular opposition parties have won only a handful of seats so far. Two candidates from the liberal Wafd Party won seats on Saturday.
Monitors said NDP supporters and the Brotherhood had brawled in places. Armed thugs attacked Brotherhood supporters with machetes in at least one town, witnesses and the victims said.
Police also tried to stop journalists reporting freely.
"The aim was to prevent voters from reaching the ballot boxes and to affect the result. But with perseverance the people and the Brotherhood were able to overcome the barriers"
Brotherhood deputy leader
Reporters working for the French agency AFP, Reuters, the BBC and the US-based Associated Press all said they had been harassed or had equipment or papers seized.
The Brotherhood, which advocates political freedoms and wants to bring legislation closer to Islamic law, is fielding candidates for 49 of the 136 seats at stake in the final round of the elections beginning on 1 December.