The principle of recouping the additional payments, which the government has estimated at around €140 million, was included in the 2017 budget, approved by Portugal's parliament in December 2016.
The measure aims to minimise annual electricity price rises agreed by the previous government with international creditors in order to eliminate Portugal's €5 billion electricity deficit.
A deficit accrued because consumer prices did not reflect all the costs of electricity generation, including subsidies to producers.
Wind was Portugal's second largest renewable energy source in 2016, behind hydro power.
"This is a retroactive measure, and any such measure reduces investor confidence," Antonio Sa da Costa, president of Portuguese renewables sector association Apren, told Windpower Monthly.
"Some wind producers have already said they won't be making any further investments until this issue has been clarified," he said.
"It could cost a lot in lawyers and court fees," he predicted. The additional payments were legal at the time they were made up to 2007.