PCGG Commissioner Ruben Carranza Jr. said the agency cannot ascertain the exact amount of the deposits, but said the total was conservatively estimated at $1 million in 1986.
"The deposits had been moved before a freeze order on all the Swiss accounts of the Marcoses and their cronies was issued," he said.
Disini’s wife, Pacita, is a cousin of former First Lady Imelda Marcos.
The current leadership of the PCGG stumbled upon the Disini deposits while reviewing the records of the agency.
Earlier, the PCGG also filed forfeiture cases against four other cronies, including Geronimo Velasco, a former energy minister of the late strongman Ferdinand Marcos.
Disini is facing two criminal cases before the Supreme Court in connection with the mothballed Bataan Nuclear Power Plant (BNPP) project.
A project of the National Power Corp. (Napocor) under the Marcos administration, the BNPP was never commissioned due to structural defects.
Disini and his wife had been accused of bribing Marcos into awarding the BNPP contract to the US firm Westinghouse Electric Corp.
The businessman was also accused of corrupt practices for his role in the project perceived to be grossly disadvantageous to the government.
In 1993, Ombudsman Aniano Desierto dismissed the bribery charge for lack of evidence. Four years later, the corruption charge was also dropped.
This prompted the PCGG to elevate the cased to the Supreme Court. Just recently, the PCGG asked the high tribunal to immediately resolve both cases, saying the government continues to shoulder the BNPP debts.
Carranza said that this year alone, the government will have to shell out $43 million for foreign debt servicing and P134 million for domestic debt servicing.
So far, the government has paid some $1.9 billion for the BNPP loan. Debt servicing will continue until 2018.