The funds will be allocated by the NSRF and add up to 80 million euros.
Businesses that can apply include hotels, rooms-to-let and catering enterprises on island regions.
According to the ministry, businesses located or stationed on islands with fewer than 3,100 residents will be charged no interest rate.
The loans can be used for investment and operating costs (replacing equipment), redecorating or for the promotion of local products.
The necessary requirements of the tourism businesses that wish to apply will be announced on 15 March 2013.
The program will be implemented by the General Secretariat of the Public Investment Fund and the Hellenic Fund for Entrepreneurship and Development (ETEAN).