Support for renewables is currently financed through contributions based on electricity consumption through a levy on energy bills.
The scheme, which will apply until December 2029, will benefit companies in Slovakia that have high electricity usage and more exposed to international trade, with a provisional budget of €120 million (£106m) for 2019 to 2021.
They will receive compensation for up to a maximum of 85% of their contribution to the financing of support for renewable energy.
The Commission said: “The Commission found that the compensation will only be granted to energy intensive companies exposed to international trade, in line with the requirements of the Guidelines.
“Furthermore, the measure will promote the EU energy and climate goals and ensure the global competitiveness of energy-intensive users and industries, without unduly distorting competition. On this basis, the Commission concluded that the measure is in line with EU State aid rules.”