The commission supported the plan at its session on Friday in Zagreb, Croatian and Slovene Economy Ministers Branko Vukelic and Andrej Vizjak respectively, said after the session.
The financial means for the implementation of the programme will be ensured from the Croatian and Slovene funds for the plant's dismantling.
The funds will be ensured with the payment of 19 annual installments, each totalling 28.5 million euros, until 2023.
Croatian Minister Vukelic said the costs would not raise electricity prices in the country.
Croatia is yet to set up its fund, while Slovenia did it some ten years ago, and has already collected 115 million euros for this purpose, according to the latest figures.
The two ministers said that today's meeting did not focus on possible radioactive waste storage sites.
Vizjak said that Slovenia had invited bids for some sites, while Vukelic reiterated the Croatian government's conclusion that there would be no plans for building a radioactive dump site in Croatia.