Bakiev left the parliament building after his speech, but legislative speaker Omurbek Tekebaev vowed to present a rebuttal to the president's address later in the day.
Bakiev suggested the parliament is turning into a place for petty arguments and charged that some deputies are using any opportunity to create "political hysteria."
"We need a strong parliament, a strong legislative body, as never before," said Bakiev, who was elected months after a popular uprising in March ousted a long-serving post-Soviet administration. "Instead, the parliament is turning into a place of political squabble, the source of an atmosphere of instability in the country."
Bakiev also told the deputies to stop their legal and illegal business activities and demanded that they not use their legislative mandates to fight off business rivals.
The Kyrgyz president said lawmakers need to devote themselves to their work in parliament, noting that no budget has been passed and privatization stalled. He said parliament "is still sabotaging the adoption of the law on privatization."
Kyrgyzstan's political atmosphere has been tense in recent weeks, particularly since two provincial governors challenged transfers ordered by the president and Prime Minister Feliks Kulov publicly accused police and security officials of failing to tackle organized crime and corruption.
Some lawmakers have suggested that the government's perceived weakness is the source of many of the current problems, rather than the legislature.
(with additional ITAR-TASS reporting)