The opposition said on Monday that the elections were riddled with abuses and were worse than the first round, which took place on 27 February.
"This is the dirtiest election I've seen," said Ishenbai Kadyrbekov, a disqualified opposition candidate.
The Organisation for Security and Cooperation in Europe (OSCE) said the first round of voting on 27 February fell short of international standards, noting instances of vote buying, questionable disqualification of candidates and interference with the media.
The government has dismissed those charges, but opposition Ata Meken Party leader Omurbek Tekebayev, who won in Sunday's runoffs, has joined in the accusation and blamed the authorities of "all the traditional breaches, like vote buying and intimidation of voters".
Edil Baisalov, head of the coalition of civic groups For Democracy and Civil Society, which monitored the vote, agreed that the runoffs were worse than the first round and marred by open and widespread vote-buying and the obstruction of election observers.
"This is the dirtiest election I've seen"
Election chief Sulaiman Imanbayev denied the allegations, saying only a few breaches were reported and would not affect the election outcome.
The OSCE sent 60 observers to monitor the runoffs and planned to give its initial assessment later on Monday.
With more than 90% of the votes counted from Sunday's polls, election officials said on Monday opposition candidates had won only four of the 43 seats at stake in the Central Asian country's parliament.
The runoffs were a crucial test of strength both for Akayev and the opposition before October's presidential election, amid opposition charges that Akayev might extend his rule beyond constitutional limits.
Akayev, who has been in power since 1990 and is not eligible under the constitution to run after serving two consecutive terms, has repeatedly denied he wants another term.
However, the opposition fears his loyalists are seeking to extend his rule or hand-pick his successor. A compliant parliament could ease the task, which could require