Economists[2] generally acknowledge Masagana 99 to have failed because the supervised credit scheme it offered to farmers proved unsustainable.

It performs these functions through various activities and strategies, which include procurement of paddy from individual farmers and their organizations, buffer stocking, processing activities, dispersal of paddy and milled rice to strategic locations and distribution of the staple grain to various marketing outlets at appropriate times of the year.

In recent years, in response to globalization and to the efforts to reduce the national budget deficit, the government has been looking into the possibility of restructuring, streamlining or privatizing certain activities of the NFA.

165 signed by President Benigno Aquino III reassigned the National Food Authority and three other agencies to the Office of the President,[5] with oversight responsibilities for the four agencies given to Francis Pangilinan in the newly created post of Presidential Assistant for Food Security and Agricultural Modernization.

Then-NFA administrator Orlan Calayag stepped down in what he described as a "courtesy resignation" so that Pangilinan could appoint his own preferred candidate to head the NFA.

[9] The Ombudsman of the Philippines’ issued a 6 months preventive suspension order effective on March 4, 2024 against Administrator Roderico R. Bioco and 138 other officials and employees, including Assistant Administrator for Operations John Robert Hermano and several regional managers and warehouse supervisors nationwide.