Around 4000 protesters gathered outside a mayor's office in the constituency of Nooken in support of an opposition candidate who came second in Sunday's elections to the 75-seat parliament, a representative of the Coalition for Democracy and Civil Society, Cholpun Argesheva, said on Tuesday.
"They were demanding the resignation of the mayor and head of the district election commission and the carrying out of fair elections," Argesheva said.
In another southern town, Aravan, around 3000 people demonstrated and blocked off a road in support of the defeated rector of the nearby Kyrgyz-Uzbek University, another observer for the Coalition for Democracy and Civil Society, Ruslan Tashenov, said.
A third protest by around 300 people continued in the border town of Kara-Suu, the coalition said.
The towns are part of a region with a substantial Uzbek minority and lie close to Kyrgyzstan's tense border with Uzbekistan, making the area a focus of concerns about potential conflict.
"They were demanding the resignation of the mayor and head of the district election commission and the carrying out of fair elections"
representative, Coalition for Democracy and Civil Society
Observers expect numerous election disputes in coming weeks as outright winners were declared in only 31 of the country's 75 constituencies, with run-off polls due on 13 March as well as first round re-runs in two constituencies.
Kyrgyzstan's election system demands that a candidate must get at least 50% of votes to win outright, with other races going to a run-off.
The election is being closely watched as a stepping stone to the 30 October presidential elections in which President Askar Akayev has vowed to stand down - potentially a first for the Central Asian former Soviet republics as none of their leaders has stood down at polls since the Soviet Union's 1991 collapse.