Matilda Concepcion-Millare and her sister Ana Marie Concepcion-Maglasang face administrative charges of dishonesty and grave misconduct as well as criminal charges for violating anti-graft laws.
They were immediately suspended, reportedly to prevent them from harassing potential witnesses and tampering with evidence.
"The Office of the Ombudsman found during the initial evaluation that the documentary proof... constitutes strong evidence of guilt for dishonesty and grave misconduct," spokesman Ernesto Nocos said.
The Department of Finance stated in its complaint that the "substantial property ownership and lifestyles of both sisters are undoubtedly manifestly out of proportion to and cannot, in any manner, be justified by their lawful income."
Maglasang allegedly owns a Ford Lexus and a Ford Expedition, officials said. Her monthly salary is P16,000.
She has two real estate properties in Cainta, Rizal, and one mansion in Tagaytay City.
Government investigators also found that Maglasang owns a BMW, land in Antipolo City, Rizal, a dollar account in US bank and condominium unit in Los Angeles.
Millare has five luxury vehicles and one speedboat. She has a house in an upscale Pasig neighborhood and another in Quezon City, land in Bulacan, Sorsogon and Zambales provinces. Her monthly salary is P20,000.
In its complaint, the department said the sisters’ illegally acquired properties "should be susceptible to forfeiture and reversion proceedings" under the ill-gotten wealth law and should be confiscated by the government when a case is filed in court.