Bakiyev dissolved the outgoing chamber, packed with his opponents, in October.
He says a less unruly parliament will lead to stability.
"I am sure our new parliament will not be like the one before," he said after casting his ballot in the capital Bishkek.
"Either way it will be a new and productive parliament."
|"It seems the plan is to have one team in parliament that would vote unanimously"|
Almaz Atambayev, opposition Social-Democratic leader
His Ak-Zhol party accused the opposition parties of cheating.
"Voters were offered vodka by unknown people who said they were from the Social Democratic party in exchange for their votes," it said in a statement.
Twelve political parties were competing for the 90 seats in the Zhogorku Kenesh, the former Soviet republic's legislature.
Opposition parties denounced pressure from the authorities before the vote, including a vote ban for an opposition leader over an apparent breach of electoral law and a lawsuit launched against one of the main opposition parties.
"There is a lot of dirt and intrigue in these elections ... Our party has apparently become too powerful and has started to scare a lot of people," Almaz Atambayev, head of the opposition Social-Democratic party, said.
"It seems the plan is to have one team in parliament that would vote unanimously."Constitutional changes
The vote was necessitated by constitutional changes approved in October that were supposed to ease relations between Bakiyev and his detractors in parliament by increasing the powers of the legislature.
However, the referendum on the changes was criticised by the Organisation for Security and Co-operation in Europe. More than 250 observers from the OSCE were dispatched to Kyrgyzstan for Sunday's poll.
|Twelve political parties were competing for |
the 90 seats in the Zhogorku Kenesh [AFP]
Bakiyev says a less unruly parliament would help the government press ahead with stalled economic reforms in an impoverished country burdened by a huge external debt.
But the opposition said it feared Bakiyev might overstep the mark and block their entry into the assembly altogether.
Since assuming the presidency two years ago, Bakiyev has struggled with politicians over government appointments and the scope of presidential powers.
Opposition supporters have frequently massed in the centre of the capital, Bishkek.
Police cracked down in April, using tear gas and stun grenades to break up protests.
But opposition groups have said they will respond to any election fraud by taking to the streets again.