Germany, to support wind, solar and other renewables under its nuclear phase-out, imposes a surcharge on electricity bills but reduces this levy for energy-intensive companies that face international competition.
The European Commission said it had launched an enquiry following "numerous complaints ... From consumers and competitors" to assess whether the discount amounts to state aid and an unfair advantage for some companies.
Merkel, speaking to parliament today, denied that the rebate distorts competition and warned that scrapping it would hurt German businesses and cost jobs in Europe's largest economy.
She said Berlin would work closely with the Commission on the issue but stressed that it would "make clear that Europe will not be made stronger by threatening jobs in Germany".
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The Commission said in a statement that "the surcharge reduction for energy intensive companies appears to be financed from a state resource".
Furthermore, the "reductions seem to give the beneficiaries a selective advantage that is likely to distort competition within the EU internal market".
The EU executive said it also had concerns over the lower surcharges offered to German energy suppliers sourcing 50 percent of their electricity from domestic sources, saying this may discriminate against imported electricity.
The opening of an in-depth enquiry allows third parties to comment but it does not prejudge the outcome of the investigation.
The Commission launched a first enquiry earlier this year into the green energy law from 1998 that was revised last year after Germany decided to abandon nuclear energy in the wake of the 2011 Fukushima disaster.