The surplus rose from Rs 203.50 crore in the financial year ended March 31, 2015 to Rs 356.19 crore in 2015-16.
The total income jumped to Rs 601.67 crore last fiscal from Rs 513.17 crore in 2014-15.
CAG, which examined Sebi's records, said the income is overstated by Rs 1.66 crore being excess booking of income on accrual basis in 2015-16, representing fees realisable by Sebi from FPIs, which actually pertains to registration and renewal fees for the periods commencing in/after April 2016.
Sebi has advanced a sum of Rs 222.83 crore to the National Institute of Securities Markets (NISM) -- a public trust established by it -- in 2013-14 to 2015-16 towards cost of building a campus at Patalganga on lease basis.
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The interest earned on these advances amounting to Rs 2.17 crore has not been accounted for by the regulator in its books, resulting in understatement of 'interest earned', 'capital advances to NISM' and 'surplus' by Rs 2.17 core, CAG said.
The physical verification of inventory like books and publication, stock of paper, stationery and other consumables has been carried out for the year 2015-16.