Where do I complain about a Sri Lankan travel agency?

If you get into really severe trouble with an operator, then your official complaint should go to the Tourist Police Division, or to the Sri Lanka Tourism Development Authority (SLTDA). Both of them have dedicated units for addressing international visitor grievances in a proper manner.

For fast, real-time on-the-ground emergencies, dialling 1912 will connect you to the official tourist hotline. Also keep records of every message, all receipts, and the contractual agreements you signed. That documentation will strongly back you up if government intervention ever becomes necessary.