Early results in the election gave the majority of votes to two parties with ties to the ruling elites amid allegations of vote buying.
Local media estimate that about 4,000 people took part in the rally in Bishkek, the country's capital. Smaller protests also took place in two other Kyrgyz cities.
One video of the protest in Bishkek showed a group of young men tried to break through the gates of a government complex that houses both the parliament and the presidential office.
Police moved to disperse the crowds in the evening, using water cannons, tear gas and flashbang grenades. Dozens of people were reported to have sustained injuries in clashes with police.
Preliminary results of the Sunday election, reported on Monday evening by Kloop, showed that only five parties out of 16 featured on the ballot won seats in the Kyrgyz parliament.
The Birimdik party which is considered pro-government, received over 26% of the votes. The Mekenim Kyrgyzstan party, linked to a former top customs official, won over 24% of the votes. Three more parties have passed the 7% threshold to gain seats in the parliament.
The election-monitoring body of the Organization for Security and Cooperation in Europe said in a report on Monday that “fundamental rights and freedoms were overall respected" in this year's election in Kyrgyzstan, but that “credible allegations of vote buying remain a serious concern."
Local media reported that 12 parties have signed a document Monday demanding the authorities to cancel the results of the election and hold a new one.
“We all have witnessed a true lawlessness during the election campaign and the election day yesterday ... Pressure on the voters, intimidation of the voters, bribing,” Klara Sooronkulova, leader of the Reforma opposition party, said.
“We have talked with all opposition parties and created an opposition coalition. We’re now forming a coordination council and demand that the Central Election Commission cancel the (results of the) elections within 24 hours," added Zhanar Akayev, a lawmaker on the ticket of the Ata Meken opposition party.
“We also demand that the Central Election Commission hold new elections. We have to hold new elections within a month,” Akayev said.
According to media reports, the unrest in Bishkek continued well into the night. Late Monday, the winning Birimdik party said it was ready to take part in a new election, should one be scheduled, and urged other parties who won seats in the parliament to do same.
Kyrgyzstan's President Sooronbai Jeenbekov called a meeting with all 16 parties on the ballot for Tuesday morning.