The bank had registered a net profit of Rs 59.44 crore in the corresponding period of the previous fiscal.
The bank had also posted a loss in the sequential quarter ended March 2016 at Rs 119.84 crore.
Total income of the Pune-based lender fell to Rs 3,444.15 crore in first quarter of 2016-17, from Rs 3,526.13 crore in year-ago period, it said in a regulatory filing.
Provisions for bad loans and contingencies almost doubled at Rs 842.50 crore for June quarter, from Rs 483.91 crore a year earlier.
Value-wise, the gross NPAs in the respective quarters were Rs 13,039.63 crore and Rs 7,574.86 crore.
Net NPAs rose to 8.73 per cent (Rs 8,609.44 crore) from 5.04 per cent (Rs 4,708.11 crore).
Earnings per share fell with a loss of Rs 3.40 during June quarter, against a gain of Rs 0.56 in the year-ago quarter.
Bank of Maharashtra shares were up 2.25 per cent to close at Rs 31.75 on BSE.
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