They were among 15 firms whose cases were dropped by Riau provincial police earlier this year due to insufficient proof, sparking protests and prompting the parliamentary commission for law, human rights and security to set up a task force to examine the controversial decision.
Ms Siti told the working committee that her ministry has revoked the licences of three companies: Dexter Timber Perkasa, Siak Raya Timber and Hutani Sola Lestari.
It has also temporarily suspended the operations of Sumatera Riang Lestari, and ordered another firm Rimba Lazuardi to comply with conditions such as being equipped to monitor potential fires and to manage them if they occur.
The Riau legislative council members and green groups were summoned to give evidence to the committee.
The committee will present its findings to Parliament and recommend that police restart investigations if evidence of violations by any company is found.