The dispute boiled over on the weekend, when roughly 25 supporters of Media-Invest, a firm that owns a 50 percent stake in Pyramid, tried unsuccessfully tried to storm Pyramid's offices in Bishkek.
Illarion Adamyan, a legal advisor for Media-Invest, denied accusations that Maksim Bakiev, a son of the president, is involved in the conflict.
Media-Invest accuses current heads of the television channel of mismanagement.
Bakiev has tasked Deputy Prime Minister Adakhan Madumarov with investigating the clash while a parliament commission is created to look into the dispute.
A group of Pyramid employees and supporters from different media outlets rallied in front of parliament on 12 December, protesting what they say is an attempt to silence their reporting.
They also said that they do not believe Madumarov is impartial.
Pyramid's head, Elina Chernyavskaya, believes the clash was prompted by Pyramid’s critical coverage of Bakiev's government.