Zenaida Sarmiento, an acting special collecting officer, was also charged with malversation of public funds before the Sandiganbayan and her benefits forfeited.
Ombudsman Simeon Marcelo said Sarmiento was found guilty of grave misconduct after being heard in an administrative proceeding.
"The presumption under the law that she used and converted the public funds for her personal use was not duly controverted," Marcelo was quoted by Office of the Ombudsman spokesman Ernesto Nocos.
"Sarmientos act constitutes the very essence of grave misconduct, which could not be countenanced, considering that she was an accountable officer occupying a sensitive position dealing with public money."
The Commission on Audit had filed the complaint against Sarmiento after she ignored demand letters that she explain why she failed to account for P4.2 million in duties and taxes between November 1996 and July 1998.
Sarmiento was only able to account for 365 pieces of the 374 official receipts for duties and taxes issued to her by Customs, the office of the Ombudsman said.
Sarmiento also failed to include the missing receipts in her report of collections, Nocos added. Delon Porcalla