 In 2014, the National Bureau of Investigation filed graft charges before the Ombudsman against Banayo and five others in connection with the alleged irregular rice importation program of the agency during his Tenure


In September 2012, Banayo resigned from his NFA post to prepare to contest the May 2013 House of Representatives mid-term elections in Agusan del Norte.Orlan Calayag was appointed to succeed him in January 2013.In December 2012, 4 SM Agri Venture Multi-Purpose Cooperative head Simeon Sioson claimed in testimony before the Senate that Banayo and Nixon Kua had been involved in rice smuggling.