Among the pieces that Bautista managed to sell was "Le Bassin aux Nympheas" by Monet, from his famed water-lily series, that netted $32 million (£19.5 million).
That one can't be recovered but the Philippines is determined to get back three unsold paintings that Bautista had in her possession: another Monet, "L'Eglise et La Seine a Vetheuil," Alfred Sisley's "Langland Bay" and Albert Marquet's "Le Cypres de Djenan Sidi Said".
"We want the three paintings back," Andres Bautista chairman of the Presidential Commission on Good Government, told reporters in Manila.
"We will recover them. They were acquired with state funds so they belong to the Filipino people," he said.
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Andres Bautista is not related to Vilma Bautista.
Andres Bautista said the government would file a civil case in New York to recover the paintings. He did not give an estimate of their value.
Bautista headed an agency tasked in 1986 with recovering about $10 billion of ill-gotten wealth of the Marcoses and their cronies. He said about 150 works of art were being sought.
"This will take time, it may take a lifetime," he said.
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Vilma Bautista was convicted in November of conspiracy and tax fraud charges related to the sale or attempted sale of four museum-quality paintings acquired by Marcos during the two decades that her husband was president of the Philippines.
The art disappeared around 1986, when Marcos was ousted in a popular uprising. He died three years later in Hawaii.
Bautista sold Monet's "Le Bassin aux Nympheas" for $32 million to a London gallery.
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Imelda Marcos, 84, has been charged with civil and criminal crimes, but never been jailed despite evidence of massive wealth accumulated during her husband's 1965-1986 rule, most famously in the form of her huge collection of designer shoes.
She is a congresswoman and has denied that her family's wealth was ill-gotten.