The court allowed South Premiere Power Corp., a unit of San Miguel Corp to suspend a power supply agreement with Manila Electric Company (Meralco) after the companies were prevented from raising tariffs by the regulator.
"We hope that the CA (Court of Appeals) will reconsider and include in their deliberations the extremely deleterious effect this will have on power prices for ordinary Filipinos," Marcos was quoted as saying, describing the decision as "unfortunate".
South Premiere and Meralco had sought to raise prices amid higher costs of coal, which the Energy Regulatory Commission rejected in September citing fixed prices set under power supply agreements.
Marcos, who began his six-year term in June, has promised lower electricity rates, which are among the highest in Asia. Higher electricity prices would put further pressure on Philippine inflation, which hit the fastest pace in nearly 14 years last month.
San Miguel, the Southeast Asian nation's largest conglomerate and one of its major power producers, has said it needs "temporary relief" to allow it "to sustainably provide for the increasing power needs of our country while meeting our obligations to our various stakeholders".
It told the Philippine Stock Exchange on Friday it had received a copy of the court's resolution.
Meralco, the country's biggest power distributor whose franchise covers metropolitan Manila and nearby provinces, said it was "reviewing the resolution in consultation with our counsel to determine the next steps".
(Reporting by Enrico Dela Cruz;Editing by Elaine Hardcastle)