Sister Christine Tan, who could have chosen to live a life of comfort with her wealthy family, died at around 5 a.m., according to her staff at the Religious of Good Shepherd convent. She was 72.
Details about her death were not immediately known.
Tan underwent surgery last March for stomach cancer and recovered but her health slowly deteriorated later.
In 1998, Estrada appointed Tan as chief of the Philippine Charity Sweepstakes Office.
She shot to prominence in 2000 when she accused the former film actor and his family of cornering a lions share of the PCSOs funds set aside for charity institutions for their own supposed charity projects.
Tan and three other members of the five-member board were promptly sacked.
Tan is the fifth in a brood of seven that included former ambassador and former Bureau of Internal Revenue chief Bienvenido Tan.
A sickly Tan was reportedly turned down twice when she tried to become a nun. Her persistence paid off on her third try.
Tan devoted her life helping ease the plight of the poor, particularly in the slums of Manila.