Sources said the agency has got evidence which show that the flat was allegedly purchased by her using false declaration and by hiding information about the flat alloted to her under government quota and the land possessed by them.
Her father Uttam Khobragade, a Maharashtra cadre IAS officer, is a former CEO of Maharashtra Housing and Area Development Authority (MHADA).
As part of its investigation, CBI is probing alleged illegal beneficiaries and benami property holders in the housing scam.
Controversial diplomat Devyani, India's then deputy consul general in New York, was arrested by the United States authorities in December last year over alleged visa fraud which triggered a diplomatic row between the two countries.
She was transferred back and is now posted in India.
Under the CBI scanner are nearly 25 alleged illegal beneficiaries who were allotted flats in the Adarsh Housing Society which was said to be constructed in violation of norms.
Retired High Court Judge J A Patil's report on the alleged scam has opened a can of worms bringing out alleged irregularities in the allotment.
The agency sources said they have got documents showing that Devyani had allegedly been allotted a flat in another government housing society in Oshiwara in 2005.
The sources said according to the rules of Defence Estate, members cannot get flats in two housing societies which get land on concessional rates.
Patil report had termed 25 out of 102 members of the housing society as ineligible.
Meanwhile, Uttam Khobragade refuted CBI's charge saying Devyani was not responsible for making the declaration and it was done by him.
"I had made the declaration and not Devyani. She was not even aware of what I said in the declaration. So how can Devyani be responsible for any wrongdoing" he said.
"The declaration where I have said that Devyani is not an owner of any flat in Mumbai is dated July 29, 2004 and at that time Devyani did not own any flat in Mumbai. So, there was no falsehood in the declaration," Khobragade said, adding the possession of a flat in Meera Co-operative Housing Society was given to them only in May 2005.
He said when Devyani had applied for a flat in Adarsh, the Society was told categorically that she was just a member of Meera Housing Society and not a flat-owner and that she would resign from the Society when allotted a flat in Adarsh.
Khobragade said the flat in Meera Society was sold as soon as Adarsh accepted Devyani's membership and the proceeds were used to pay for the apartment in Adarsh.