Making a surprise appearance at the opposition rally in Bishkek, Kurmanbek Bakiyev was booed and whistled at by about 10,000 people.
"I am not Akayev, I will not run away from my people, I am not afraid," President Bakiyev said before walking away, heckled by the crowd.
Kyrgyzstan has been volatile since Bakiyev came to power last year after a coup that ousted Askar Akayev.
Last July, Bakiyev won the presidential election by a landslide, pledging to bring order and democracy.
The opposition, led by Omurbek Tekebayev, a former speaker of parliament, demand that Bakiyev limit presidential powers as promised during the election, give more authority to parliament and the prime minister, and eradicate corruption and crime.
Earlier this week Bakiyev threatened to use force to prevent any attempt to unseat him during Saturday's protest.
"Down with corruption" and "We have lost all hope", read the banners carried by protesters chanting, "Bakiyev is the new Akayev!" as they marched towards Bishkek's main square, which was guarded by 5,000 police.
"Our revolution is continuing. It has not ended yet. Bakiyev's rule today is Akayev's yesterday"
Roza Otunbayeva, former minister
The mountainous nation, with more than half of its five million people living in poverty, has been shattered by violent clashes for controls of local markets, and waves of jail riots. Several parliamentarians have been killed.
Protesters included some former Bakiyev allies who joined the new opposition, disenchanted with what they see as his backtracking on pledges of order and democratic reforms.
Roza Otunbayeva, who served briefly as foreign minister in Bakiyev's cabinet, said: "Our revolution is continuing. It has not ended yet. Bakiyev's rule today is Akayev's yesterday."
Felix Kulov, the prime minister, was standing next to the president and was given a warm reception by the crowd.
Kulov, a former security services boss, is widely respected for his tough actions to restore order in the country after two nights of looting after Akayev's departure.
"Your demands are being heard," he told the crowd.
In a move seen as an attempt to win Russia's support amid rising tensions at home, Bakiyev has threatened to shut down the US air base and blamed certain "foreign forces" for stir up unrest in country.