Andres Bautista said the list of paintings including ones by Van Gogh, Rembrandt and Michelangelo was compiled from various documents after a 1986 "people power" revolt ended dictator Ferdinand Marcos' 20-year rule and sent his family into exile in Hawaii.
During Marcos' two decades in power, Imelda Marcos became known for excess, symbolised by her large shoe collection. The family is accused of illegally amassing billions of dollars' worth of wealth.
"We think that actually there are more paintings that are not in this list," he told reporters. "We just don't have the evidence to prove our case."
He said his agency had a budget of 106 million pesos ($2.3 million) last year, and "given our limited resources ... We don't have the wherewithal" to track the paintings.
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Among the paintings not on the list is one by Claude Monet that was sold for USD 32 million in 2010 by former Marcos aide Vilma Bautista, he said. The aide was sentenced this month by a New York court to up to six years' imprisonment for conspiring to sell the art work and tax fraud.
The two Bautistas are not related.
Earlier this month, a Philippine anti-graft court ordered Imelda Marcos to relinquish more than USD 100,000 in jewelry after ruling it was ill-gotten. It was the third collection of Marcos jewelry that the government has acquired.
The two other collections are estimated to be worth up to USD 8.4 million.
The government has recovered 164 billion pesos (USD 3.7 billion) of Marcos' alleged hidden wealth over the years and is targeting at least 50 billion pesos (USD 1.1 billion) more.
The Marcoses have denied any wrongdoing.