In a hastily called press conference, Yap said he was stepping down to clear his name from tax evasion charges and that he did not want the investigation involving his family to cause further damage to Mrs. Arroyos troubled government.
"It was a personal decision for me to quit. It has occurred to me that my continued stay at the department is not tenable considering my personal circumstances," said Yap, adding he would stay on until a replacement is found.
Meanwhile, the Palace branded as "disinformation" reports that the President was about to carry out a major Cabinet shakeup claims said to be bolstered by Yaps resignation.
Press Secretary Ignacio Bunye said these reports were "grossly exaggerated" and that it was unfair to make premature announcements about some Cabinet officials getting the axe.
"Although we know its the Presidents prerogative to make new appointments anytime, reporting the names of those who would be possibly replaced was baseless," the Presidents spokesman said.
What Bunye confirmed was that the Palace was recruiting Mike Toledo, former press undersecretary of deposed President Joseph Estrada, to become part of the Office of the Press Secretary.
"Negotiations" on this, he said, were still ongoing.
Bunye and presidential political adviser Gabriel Claudio said Yap was an asset to the administration, but his decision must be respected.
"Secretary Yaps situation is unique. Given his personal circumstances, his resignation to clear himself of tax charges is commendable," Bunye said.
"His record of performance as National Food Authority Administrator and more recently as DA secretary is beyond reproach," he added.
A key adviser to the President, Rep. Joey Salceda, said Wednesday that the President was expected to make 10 major announcements in the coming weeks, including a Cabinet reshuffle, giving her the opportunity to "remove people who erode her credibility."
Yap insisted, though, that his resignation was not in response to mounting pressure on the President and her allies to step down amid allegations of fraud during last years presidential race.
Yap said he talked to the President on Wednesday night and asked her if there was basis for talks circulating that he would be one of those targeted for the planned Cabinet revamp.
"The President expressed her full trust and confidence in me, but I felt under the circumstances that I should quit to spare her administration from more problems and embarrassment. Ayaw kong maging pabigat sa President (I dont want to be a burden to the President)," Yap said.
Yap, 39, was a former student of Mrs. Arroyo in economics and reportedly one of her closest Cabinet members. He denied any wrongdoing in a recent tax evasion case against him involving a corporation owned by his family, but he said staying on at his post would be a "no-win situation for myself and the President that I serve."
Claudio said there was no other way to interpret Yaps decision other than that he was in a "crucial situation peculiar to him."
"It has nothing to do with political controversies. Im sure thats nothing to do with the President," Claudio said when asked if Yap quit because he no longer wanted to support Mrs. Arroyo following her admission that she improperly phoned an election official, supposedly to protect her votes during the May 2004 polls.
Claudio was surprised when reached for comment on Yaps resignation, saying the DA secretary never mentioned it to him when they were together a few days ago.
"His colleagues are saddened by the development," Claudio said.
Bunye also said Yaps resignation had nothing to do with the decision of First Gentleman Jose Miguel "Mike" Arroyo to go into exile abroad since Yaps appointment was not because of any association with the Presidents husband.
"In fact, it was on personal invitation of the President," Bunye said.
According to Bunye, Yaps decision to stay on until a replacement has been named reflects his professionalism and deep concern for the image of the department.
"We wish him well and we know he will always be at the service of our farmers, fisherfolk and the Filipino people even in a private capacity," he said.
Yap similarly denied any "perceived" links to Mrs. Arroyos husband.
"I never met the First Gentleman until I joined the government and saw him on social occasions," he said.
According to Yap, had he elected to remain in government and be cleared of the tax evasion allegations, there probably would be allegations of a whitewash.
"And if state prosecutors find probable cause and file charges in court, I risk embarrassing the government, which is the last thing the government or she (Mrs. Arroyo) needs at this time."
Two weeks ago, the Bureau of Internal Revenue (BIR) filed tax evasion charges against Yap and his father, Domingo H. Yap of DHY Realty, on grounds of non-payment of withholding taxes for three consecutive years from 1997. The Yaps were also accused of not paying the correct documentary stamp tax on the purchase of a 3,176-square meter property in Pasig City.
Yap, in defense of his family, explained that the transaction occurred with full transparency and in accordance with law.
Yap was the first government official charged by the BIR with tax evasion following a controversial and high-profile tax evasion crackdown that targeted local entertainers such as Richard Gomez, Regine Velasquez and Judy Ann Santos.
Congressmen also expressed regret over Yaps resignation, but they lauded his "sense of delicadeza and sterling performance" during his stint at the DA.
Rep. Benasing Macarambon of Lanao del Sur said Yaps competence as DA chief had been proven by the record growth in the agriculture sector last year despite the series of typhoons that hit the country.
"Secretary Yap, one of our youngest Cabinet members, has accomplished so much in the short period that he headed the DA. We hope the President can find an appropriate replacement who can be as competent as or even better than him," said Macarambon, chairman of the House committee on agriculture and food.
Committee vice chair Rep. Edwin Uy of Isabela said Yaps decision to leave was regrettable, citing the reforms and programs he had initiated at the DA.
Uy said Yaps resignation "will certainly trigger a revamp" in the Presidents Cabinet although he noted this is already underway "to fulfill her promise for more meaningful reforms."
At the Senate, members of the chamber called for the resignation of all Cabinet members and allies of the President following Yaps resignation.
Senate Minority Leader Aquilino Pimentel Jr. said he expects more resignations to occur, including four Cabinet members whom he did not name. Pimentel, a vocal critic of Mrs. Arroyo, said the revamp story was concocted by the administration to cover up the number of Cabinet members who want to resign due to the controversies hounding the President.
He said the resignations will come one by one and that it would only be a matter of time before Mrs. Arroyo steps down.
For his part, Sen. Panfilo Lacson said he expects the administration allies to be forced by their consciences to resign because of what he said was an admission of guilt by Mrs. Arroyo for her part in rigging last years elections.
"If the other members of the Cabinet believe that they could no longer defend the President because of the cheating during the last elections, if there is any decency left in them, they should all resign," Lacson said.
In a statement released to the media, Mendoza said he would stay on until the President says otherwise.
Mendoza said his service as secretary of the Department of Transportation and Communications (DOTC) is at the discretion of the President.
"I serve at the pleasure of the President and my appointment as a government head is based on the Presidents confidence in me. As a public servant, I serve in the interest of the Filipino people with my utmost responsibility and integrity," Mendoza said.
Rumors spread yesterday that Mendoza had already resigned. According to sources, his exit had been due to the numerous scandals facing the Arroyo administration.
But Mendoza said he continued to support the Arroyo presidency.
"This is to express my full support to President Gloria Macapagal-Arroyo and to the duly-constituted authority," Mendoza reportedly said through a source at the DOTC.
Mendozas closest allies also denied their boss had been resigned.
According to DOTC Assistant Secretary for planning and projects development Robert Castañares, this simply was not true.
"I dont know where that started. It is not true. He would have informed us by now," Castañares told the press.
DOTC spokesman Thompson Lantion issued the same denial. With reports from AFP, AP, Marvin Sy, Sandy Araneta