The houses are worth a total of 43.8 million pesos ($1.1 million), the government said.
The move ends a legal battle that began in 1987, a year after her late husband Ferdinand Marcos was toppled from power, said Nick Suarez, spokesman for the government's Presidential Commission on Good Government.
Suarez said it was not known whether the Marcos family had ever lived in the houses, which will provide compensation for 10 million pesos taken illegally from the state rice importing agency in 1983.
"It is a victory for the Filipino people and the government because we were able to recover what is stolen," Suarez told AFP.
The commission has been seeking to recover the billions stolen by the late dictator and his family during his 20 years in office.
A special anti-graft court ruled in April that the family must return the money to the government, plus interest, and the same court ruled this week that the government may now seize the properties after the family failed to pay.
Spokesmen for Imelda Marcos could not be contacted for comment. Ferdinand Marcos ruled the country from 1965 to 1986, much of this time as a dictator. His family and their allies are accused of stealing billions of dollars in state funds during this period.
Imelda Marcos was known for her lavish, jetset lifestyle despite the nation's poverty and a massive collection of thousands of her shoes was found at the presidential palace after the family fled to the United States.
The commission has said that it has recovered more than 85.64 billion pesos in Marcos funds since 1986.
However the officials said the lack of a paper trail and delaying tactics employed by lawyers for the Marcos estate had prevented the commission from recovering more.
The fallen dictator`s family returned to the Philippines after his death in 1989 and have regained some of their influence in recent years.
Imelda Marcos and their son, also named Ferdinand, were elected to parliament last year. (SYS)
Editor: Ade P Marboen
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