Authorities said they did not rule out holding another vote.
The thousands-strong protests broke out after two establishment parties, one of which is close to President Sooronbai Jeenbekov, swept Sunday’s vote, according to preliminary results.
Protesters demanded that the vote results be canceled and the Central Election Commission said on Tuesday it would consider their request, local news website 24.kg reported.
Russian news agency RIA quoted Jeenbekov’s spokeswoman as saying he also did not rule out annulling the results of the contested election.
Police had dispersed the protest late on Monday, but protesters returned to the central square of capital Bishkek hours later and broke into the building that houses both the president and parliament, the local websites said.
The building known locally as the White House briefly caught fire on Tuesday morning which was quickly put out.
Protesters then broke into the headquarters of State Committee on National Security and freed former president Almazbek Atambayev, who was sentenced to a lengthy prison term this year on corruption charges after falling out with Jeenbekov, his successor.
Jeenbekov said late on Monday he would meet on Tuesday with the leaders of all parties that had taken part in the election.
Meanwhile, opposition groups appointed their own acting head of national security and acting prosecutor general and named a commandant of Bishkek although it was unclear how much actual power they wielded.
One person has been killed and hundreds wounded in the overnight clashes, the government said.
The Central Asian country of 6.5 million, which is closely allied with Russia, has a history of political volatility. In the past 15 years, two of its presidents have been toppled by revolts