It has also started a tax enquiry in case of two serving members of Sebi.
It said the proceeding had been initiated to scrutinise the tax return of Bhave for 2009-10 assessment year and the case was randomly picked up by the computer.
The notices were issued to Bhave on September 14, 2010 and January 24, 2011, when he was at the helm of Sebi.
The department said the move was not intended at harassing or victimising Bhave, and it was not acting upon some complaints against him.
It also said there was no link between the on-going tax enquiry and the issue of Bhave's extension.
"The tax proceedings in case of Bhave are routine and have no connection with any complaint or his tenure as Sebi chairman," the Central Board of Direct Taxes said.
About the enquiry on two existing members, it said necessary action was being taken according the law on the basis of complaint received against them.
Bhave was appointed Sebi chairman in February 2008 for three years. Initially, there were expectations that he might get extension, but in January, the government announced the appointment of U K Sinha as Sebi chief for three years.
Bhave was Sebi's senior executive director from 1992 to 1996.
Later, he became the chairman and managing director of National Securities Depository Limited before coming back to head Sebi.
During his tenure as Sebi chief, he took many tough decisions, including a ban on entry load for mutual funds and raised the issue of jurisdictions over unit-linked insurance products that led to a spat with the insurance regulator.
Last week, a former member of Sebi had alleged that the board of the market regulator 'abused' its powers to protect Bhave from being subjected to any independent inquiry with respect to his actions as NSDL chairman in the IPO scam, which related to irregularities in share allotment in various initial public offers between 2003 and 2006.
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