The financial operation of HELMEPA is implemented in accordance with the annual Budget, which is approved each year by the BoD and verified by auditors Moore Stephens SA. The latter submit their Report and Financial Statement to the General Assembly of HELMEPA Members.

The operation is financed by the Membership fees of the volunteer-members of the Association and donations. The annual Membership fee, excluding seafarers-Members, is set by the General Assembly and is altered every year in accordance with the official rate of inflation announced. For 2011 the Membership fee is set at € 1,490.00.

The cost of the Maritime Sector activities usually covers 80% of the total Budget , while the remainder 20% covers the activities of the Public Awareness Sector, under which operates the "HELMEPA Junior" Program. The late Captain Vassilis C. Constantakopoulos with the enthusiasm that characterized him, along with his company Costamare Shipping Co SA, offered his moral and financial support to the “HELMEPA Junior” program since its beginning in 1993. Now, his children continue his initiative for the environmental awareness of the younger generations.

The Lloyd's Register Educational Trust contributed financially in the period 2008-2011 to the enrichment of the program and the additional participation of  1,000 children members across the country.