According to the watchdog, Claro acted illegally by signing exclusive contracts with the owners of land where the company's broadcast towers are located, impeding other local mobile providers.
The fine follows complaints made in 2012 by state-backed rival operator CNT.
Claro has complained that the authorities are being inconsistent, calling the move "unjustified and disproportionate".
With about 64% market share, Claro is the largest mobile company in Ecuador and is owned by Mexican billionaire Carlos Slim.