"All night the electoral committees in the different constituencies have produced results and then changed them," senior Brotherhood official Essam el-Erian told AFP.
"These elections are rigged and invalid," he added.
Brotherhood spokesman Walid Chalabi said the group had failed to win any seats outright in the first round of voting and that just 21 of its 130 candidates were sure of making it into next Sunday's second-round run-offs.
In the last parliament, the Brotherhood, which fields its candidates as independents to get round a ban on religious parties, held 88 seats -- a fifth of the total.
Final results from the first round were not expected before Tuesday but initial indications showed the ruling National Democratic Party (NDP) of President Hosni Mubarak had made large gains in the 518-seat parliament.
In the run-up to Sunday's vote, the Islamists were targeted in a systematic crackdown by the authorities, which saw at least 1,200 of its supporters arrested, more than a dozen candidates disqualified and 11 members sentenced to two years in jail for campaigning and handing out leaflets.
"Yesterday, fraud took place in the polling stations, while the ballot boxes were being transported to counting centres and in those centres," said Hamdi Hassan, who lost his seat in the Mediterranean city of Alexandria, an Islamist stronghold.
Despite losing out to the ruling party, he said the Islamists had "won the respect of the people, their trust and increasingly their sympathy after what they saw yesterday."
A Brotherhood campaign official in Alexandria said vote rigging had been widespread.
"These elections took place in complete darkness, without any surveillance except by the NDP," Medhat al-Haddad told a press conference after the close of polls.
Authorities put turnout in the election at around 10 million but the head of the Egyptian Organisation for Human Rights, Hafez Abu Saada, said no more than 15 percent of the country's 41 million registered electors had cast a vote.
Bahey el-Din Hassan, a member of a coalition of human rights groups that monitored the vote, said: "Yesterday, there was no election. There was chaos, thuggery and violence."
A Western diplomat echoed the criticism of the lack of transparency of the vote.
"You saw problems with the entire structure of monitoring, whether by civil society groups or by candidate representatives, and that was across the board," the diplomat said.
"One reason for the Muslim Brotherhood's poor showing is that the government has gone to great lengths for months to reduce the effectiveness of their campaigning, through arrests, through denial of access to the media," the diplomat added.
The government says the election was conducted fairly and that most of the complaints received so far were not substantial.
The Egyptian Coalition for Monitoring the Election said three people were killed in poll-related violence, including an Islamist shot dead by supporters of a ruling party candidate in a southern town.
But police said the only election-related death was that of a man who was shot by unknown assailants at a polling station in North Sinai and died of his wounds in hospital.
Amnesty International's deputy Middle East director, Hassiba Hadj Sahraoui, urged Egyptian authorities to open an inquiry into the deaths.
"We had killings yesterday and we urge the Egyptian authorities to investigate them," she said.
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