President Bakiyev's party has taken 71 seats out of a possible 90
Kyrgyzstan's main opposition party has failed to gain any seats in parliament, despite receiving more than 8% of the vote in recent national elections.
Ata Meken - the main rival to President Kurmanbek Bakiyev's Ak Zhol - fell foul of election laws requiring a party to win 0.5% of the vote in each region.
Officials said Ata Meken had not gained enough votes in the second city of Osh.
Earlier reports suggested the Supreme Court had cancelled the regional rule, but officials said this was not true.
Ata Meken has promised "large-scale" protests, accusing the Central Election Commission of "falsifying the results" in Osh.
"We consider these elections were conducted dishonestly, with flagrant violations of legislation," Ata Meken said in a statement.
The BBC's Central Asia correspondent, Natalia Antelava, says Ata Meken needed only 600 votes in Osh to secure the 0.5% share they needed.
Party activists claim to have proof they received at least 3,000 votes.
Reuters news agency reported that at least one member of the country's 12-strong election commission was unhappy with the conduct of the ballot.
"Everything has been rigged - I am not taking part in this," Akylbek Sariyev said at a commission meeting on Thursday.
But the commission's head, Klara Kabilova, denied the vote was rigged, saying unidentified Estonian computer hackers had caused confusion by attacking the commission's website.
Under the new constitution introduced by Mr Bakiyev in October, parties could be represented only if they passed two separate thresholds.
Firstly they needed to receive more than 5% of the national vote.
Secondly they had to gain 13,500 votes in each region - the equivalent of 0.5% of the 2.7m people registered to vote in Kyrgyzstan.
Observers criticised the system, saying it was possible that no party would ever meet both criteria - raising the possibility of an endless cycle of elections.
Following Sunday's poll, it appeared that Ak Zhol was the only party that would be represented in parliament because it was the only party to meet the regional criterion.
However, on Tuesday the Supreme Court appeared to have overturned the regional criterion - paving the way for Ata Meken to take up parliamentary seats.
But our correspondent says the court actually reinterpreted the rule, allowing parties to be represented if 0.5% of registered voters in each region supported them, rather than 0.5% of the entire electorate.
Election officials say Ak Zhol will now take up 71 places in the 90-seat parliament.
The Social Democratic Party and the Communist Party - both of which have sided with the president in the past - took the other seats.
But initial results suggested neither the communists nor the social democrats had gained 5% of the national vote.
The former Soviet republic has endured political turmoil since 2005, when allegations of a rigged ballot led to mass protests that drove then President Askar Akayev from power.