The agency said it was closely watching PT Shopee Internasional Indonesia and PT Ecart Webportal Indonesia, the domestic units of Shopee and Lazada, respectively.
Shopee, owned by Southeast Asian technology firm Sea Limited, and Lazada, a subsidiary of China's Alibaba Group, are key players in the region's e-commerce landscape.
"There are indications that Lazada has engaged in discriminatory actions that potentially hinder competition and harm customers," the agency's chairman M. Fanshurullah Asa said in a statement.
He did not disclose details of the indications, nor specify Shopee's breaches, but called both companies' violations "similar".
"If the violations are proven, Lazada could face fines of up to 50 percent of its net profit or 10 percent of its total sales, earned within the relevant market during the period of infringement," he added.
The agency will begin the preliminary hearing of Shopee's case Tuesday, he said.