The 45-year-old actor received the villa as a gift from a Dubai-based company during the assessment year 2008-09 for plugging a real estate project, I-T sources said.
In April 2009, Khan had filed returns declaring income of Rs 126.31 crore for assessment year 2008-09. He said his income was from house, property, profession, capital gains and other sources.
The actor also included the 8,500 sq ft two-storey six bedroom themed signature villa in the returns, which is a part of The Palm, Jumeirah, as a gift given to him by Nakheel Public Joint Stock Company (NPJSC) on September 16, 2007, the sources said.
According to the I-T department, the villa received by Khan under a gift deed was taxable and a notice was issued to him on November 26, 2010.
However, the actor replied saying the gift did not constitute his income from business or profession. The company also submitted a letter to the I-T department in October 2010, stating that Khan had not provided any professional services, the sources said.