In a statement, Yap described as "baseless and malicious" the charges filed against him by Department of Agriculture (DA) resident Ombudsman Marlene Garcia Esperat.
"I cannot understand why she has to file charges barely two weeks after the announcement of my appointment as secretary of the Department of Agriculture," he said.
"The total amount is not even P432 million as claimed by Esperat, but P200 million transferred to NFA through a memorandum of agreement between DA and NFA.
"I am surprised by the timing of the filing of the case, considering that this happened a year ago," Yap said.
He said of the P200-million procurement funds, only P93.8 million was used to buy fertilizer, and the balance was liquidated to the DA.
"The awards were properly conducted and the NFA worked hard to ensure that only the price most advantageous to the government was obtained in the procurement project," he said.
Yap said the fertilizers were procured at an average price of P470 per bag, significantly lower than the prevailing market price of over P500 per bag.
The bidding followed the procedure under Republic Act 9184 — the Government Procurement Act — and was held in the presence of DA regional field officers, representatives of the Fertilizer and Pesticide Authority, farmers and the Commission on Audit, he added.
Yap, along with seven DA officials and two other people were charged with graft before the Ombudsman Wednesday over the alleged illegal purchase of P432 million worth of fertilizers.
In a four-page complaint, Esperat alleged Yap and the other respondents, along with two other private individuals, should be held accountable for graft, technical malversation and gross neglect of duty in conspiring to overprice the purchase of fertilizers.
Yap said the charges were part of the "orchestrated demolition job" to destroy his reputation as a government official.
"This project (purchase of fertilizers) occurred last year and yet, she only filed this case recently, coming so soon after the announcement of my appointment as DA secretary," he said. "Clearly, this is a case of political harassment."
Esperat claimed the respondents — along with Pepito Alvarez, owner of the Philippine Phosphate Fertilizer Corp. and businessman Jesus Varela — have conspired in overpricing the purchase of P400 per bag worth of fertilizers by as much as P100.
"It is P50 to P100 over and above the regular price in the market," Esperat revealed, in what she called "unlawful negotiated procurement."
She said the purchase is in violation of the DA bidding rules, aside from the department’s "programmed project" for such purpose for last year.
"Fertilizer procurement is a DA function," Esperat said. "A negotiated procurement instead of regular procurement by bidding is a violation of the law. Negotiated procurement is only applicable for emergency purposes."
Esperat argued that NFA should not have been given the authority to purchase the fertilizers since the agency’s function is merely to buy and sell grains.
In effect, the DA-NFA memorandum for "negotiated procurement" was illegal, she said.
Esperat claimed Yap was the implementor of the illegal project and Philphos became the "favored bidder," courtesy of Varela’s connections with a certain Chito Santos.
She said Santos and Varela were "classmates." Varela was a former DA assistant for finance and administration, she said.
Among those charged were DA Undersecretary Jocelyn Bolante, Assistant Secretary Edmund Sana, Assistant Secretary Ibarra Poliquit, Benjamin Tabios, DA legal service Eduardo Garcia. DA chief accountant Ophelia Agawin, Varela and Alvarez, as owners of Philippine Phosphate Fertilizer Corp.