A small number of works were taken away from properties owned by the 85-year-old on the order of the courts.
Pieces by Picasso, Gauguin and other masters are thought to be in the possession of the family of the country's former dictator.
Mrs Marcos lived a lavish lifestyle during her husband's 21-year rule.
She is best known for amassing a huge collection of designer shoes during the family's tenure in power, but has never been imprisoned despite being charged with a number of crimes.
State authorities claim that a selection of paintings were illicitly obtained using public funds during the Marcos era, which lasted from 1965 to his overthrow in 1986. Ferdinand Marcos died in exile three years later.
The family and associates are estimated to have amassed more than $10bn (Â£6.1bn) in property, jewellery, cash and other assets during their time in power. Mrs Marcos, who was elected to the Philippine congress in 2010, has consistently denied embezzlement.
Pablo Picasso's Reclining Woman VI, Michelangelo's Madonna and Child, and a still life by Paul Gauguin are among those the Philippine courts are keen to seize.
State spokesman Nick Suarez confirmed that a number of pieces of art had been removed from Marcos properties, but they "have yet to determine which ones or how many".
The other works on the court's list are Francisco de Goya's portrait of the Marquesa de Santa Cruz, Pierre Bonnard's La Baignade Au Grand Temps, Vase of Red Chrysanthemums by Bernard Buffet, Joan Miro's L'Aube, and one of Camille Pissarro's Jardin de Kew series.
Mrs Marcos is said to be a keen art collector, and her lawyer said that the court order and seizure were "highly questionable" and there would be an appeal.
Robert Sison said that the paintings were not included in a forfeiture case which the Philippine government brought against the Marcos family more than a decade ago.
There are thought to be a total of 150 works of art in Mrs Marcos's possession, which the authorities are keen to track down.
Artworks belonging to former Philippine first lady Imelda Marcos have been seized by authorities who claim they were acquired with stolen state funds.