The boxer - who is a member of the Filipino House of Representatives, and one of the richest men in the country - has described the move as "harassment", and claims that it has forced him to take out millions of dollars' worth of emergency loans in order to fulfil pledges that he has made to help victims of Typhoon Haiyan.
The Philippine Bureau of Internal Revenue alleges that the 34-year-old paid tax at the incorrect levels during 2008 and 2009 revenue - specifically for his staggeringly lucrative fights against Oscar de la Hoya and Ricky Hatton.
The tax authorities are claiming £31 million in unpaid tax - but Pacquiao insists that has done nothing wrong having paid US taxes on his earnings.
"I am not a criminal or a thief. I am not hiding anything. I will face my problems as they come," Pacquiao said.
"I have already paid my taxes in America. Had I not paid the correct taxes they (the IRS in America) would have come after me and I would not have been able to travel there."
Pacquiao earned £13m a few weeks ago for his win over Brandon Rios in Macau - a fight which was broadcast throughout the country, with big screens even being erected in areas devastated by the typhoon to allow fans to watch the man who has become the Philippines' greatest ever sporting hero.
The boxer dedicated the win to typhoon victims - but with his accounts frozen he had to borrow £14,000 to cover pledges he'd made to help those victims, while his staff have had to go unpaid.
The Philippine government was unrepentant, however, and has denied any political motive behind the move: "We are a government of laws, not men," said the president's spokesman, Herminio Coloma.