The Philippines' Agriculture Minister Arthur Yap has resigned to contest tax evasion charges filed against him.
Mrs Arroyo's government is under mounting pressure
The move seemed designed to shore up President Gloria Arroyo's government, already undermined by allegations of vote rigging and influence-peddling.
On Monday, Mrs Arroyo admitted talking to an election official during the vote-count of last year's election.
She also said her husband, whom critics accuse of taking pay-offs from illegal gambling groups, would move abroad.
Mr Yap is one of several cabinet members seen as close to Mrs Arroyo.
"I have become convinced that I should clear my name - not as a member of the president's cabinet but as a citizen of the republic," Mr Yap told a news conference on Thursday.
But he insisted he was not guilty of tax evasion, nor was he resigning in response to the mounting pressure being heaped on the president.
'Lapse of judgement'
Mrs Arroyo, who has made the fight against corruption a key pledge of her presidency, is trying to win back public trust after a series of potentially damaging incidents.
Accused of using position to influence 2004 poll
Husband accused of influence-peddling and taking bribes
Son and brother-in-law also implicated
Family denies all allegations
On Monday she admitted to having called an election official during the May 2004 vote count, which while not illegal, is likely to be viewed by many Filipinos as unethical conduct.
Mrs Arroyo apologised to the nation for what she called a "lapse of judgement" but denied trying to influence the outcome of the poll - in which she beat the now-deceased film star Fernando Poe by more than a million votes.
Her admission came after the opposition released an audio tape in which a woman who sounded like the president could be heard speaking with a senior election commissioner.
The president's husband, Jose Miguel Arroyo, widely known as Mike, has also been accused of scandal, along with their son and Mrs Arroyo's brother-in-law.
Opposition lawmakers have accused them of taking bribes from illegal gambling syndicates - charges they deny.
On Wednesday Mrs Arroyo announced that her husband would move abroad indefinitely, in a move analysts say is an attempt to silence the president's critics.
In response to the scandals, opposition groups are increasingly calling for Mrs Arroyo's impeachment.
But analysts say they are unlikely to succeed as she enjoys majority support in both chambers of Congress.
There is growing speculation that Mrs Arroyo may soon order a major cabinet reshuffle.
But presidential spokesman Ignacio Bunye told the French news agency AFP on Thursday: "The rumours are exaggerated."
Manila's already beleaguered economy has been affected by the crisis, and the peso hit a five-month low early on Thursday, sinking to 56.19 to the dollar.