Roy's husband, Pradip Krishen, who is one of India's best known filmmakers and environmentalists, was told that the cottage was built on land earmarked for a wildlife sanctuary.
A government ruling on Thursday, the latest in a seven-year battle, said that only tribesmen with inherited plots could build on land set aside for the Pachmarhi wildlife sanctuary.
The decision by the divisional commissioner for Bhopal and Narmadapuram in the state of Madhya Pradesh means the couple faces the prospect of having their property demolished.
The area, in central India, is home to tigers, leopards, sambar deer and flying squirrels in almost 3,000 square miles of teak and sal forests.
Krishen and Roy have been accused of hypocrisy by their political foes, who claim it is a case of the liberal, literary elite saying one thing and doing another. The nationalist newspaper Pioneer said they were "grabbing tribal land".
Scoring points?
Since Miss Roy won the Booker Prize in 1997 with The God of Small Things, she has campaigned on behalf of marginalised communities.
She has challenged Indian military abuses in Jammu and Kashmir, supported a Maoist insurgency in the east of the country and opposed the eviction of tribal communities to make way for hydroelectric dams.
Krishen said his wife had not been involved in building the cottage, and accused her critics of using the dispute to score political points.
"I first visited in 1981 and came back 11 years later and completely fell in love with it because it was relatively unspoilt," he said. Krishen bought the land in 1992 and built the house before he married Roy. He claims the land was never tribal-owned. A house nearby is owned by the sister of Vikram Seth, another author, who wrote A Suitable Boy.
Krishen said, "We bought the land and seven years later were served a notice by the forest department. They said the land was notified as an intended sanctuary and national park. We were not aware of the notification. There are 2,500 houses which people have built without knowing the wildlife protection act applies. They singled us out.
"The press say it's Roy's house. It's crazy and absurd to have her involved. The hypocrisy allegations are motivated by those stung by what Arundhati writes about. They look for any opportunity to bite back. This is about taking pot shots at her."
Officials said ignorance was not a defence for breaching the wildlife protection act. Krishen said he had not yet given up and that the final decision would be made in India's High Court.
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