Bakiyev said that a new constitution, coupled with a new parliament, would help bring more stability.
"I am convinced it will be a different, an absolutely democratic and clean election. ... With the current assembly's departure we are turning a whole page in our history."
But the Organisation for Security and Co-operation in Europe (OSCE) said on Monday it was concerned at reports of ballot-stuffing and other irregularities during the nationwide referendum on Sunday.
"A high number of irregularities were reported by several domestic non-partisan observation groups," Markus Mueller, head of the OSCE Centre in the Kyrgyz capital Bishkek, said in a statement.
"Domestic observation teams reported that they observed massive ballot-stuffing by members of precinct election commissions, use of administrative resources to bring people to polling stations, obstruction of domestic observers by local authorities and members of election commissions."
Bakiyev's opponents have accused the president of conducting a power grab.
After parliament held its final session Monday, the former deputy speaker Erkinbek Alymbekov said the changes could lead to a "strict, totalitarian system of power" in the ex-Soviet republic.
Bakiyev has accused the assembly of blocking reform and provoking political crises.
But Bakiyev has been criticised for not being aggressive enough to stop political infighting and for failing to focus on urgent issues such as crime and poverty.
Others have criticised him for not dissolving parliament earlier.
Yet Bakiyev is seen as a liberal among his Central Asian neighbours, allowing a relatively free media, strong opposition and civil society in the mainly Muslim state which is home to US and Russian military bases.
In the poll on Sunday voters also backed separate amendments raising the number of parliamentary members and changing the election process from a single-constituency system to a proportional all-party list.
Analysts say that would help the newly formed pro-presidential Ak Zhol party to gain a footing in parliament.