The auditor also suggested the Food Corporation of India (FCI) to approach a consortium through the Food Ministry for allowing it to utilise short-term loan before exhausting the cash credit limit.
In the latest report tabled in Parliament, the Comptroller and Auditor General (CAG) further suggested the FCI to get permission again to obtain guarantee for issue of bonds so as to gain access to cheaper source of funds.
"On an average, only 67 per cent of subsidy claimed was released by the Government of India over the last five years because of which FCI had to borrow from other costlier means of finance resulting in heavy interest burden of Rs 35,701.81 crore during 2011-16," the CAG said in the report.
FCI had claimed a subsidy of Rs 4,45,809.59 crore during 2011-16. Out of which, it received only Rs 3,00,675.88 crore from the ministry.
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But the agency's foodgrain procurement, distribution and other administrative costs had amounted to Rs 6,33,788 crore in the review period.
However, last year's situation was better than previous years. Reimbursement during last year was slightly better, he said, adding that the finance ministry releases less funds towards subsidy because they have competing priorities.
The government's food subsidy would have been less by about Rs 35,700 crore over the past five years if it had given money in time to FCI rather than paying interest on market loans, he added.
FCI was paying interest between 10.01 per cent and 12 per cent on cash credit, resulting in extra burden on government exchequer, it said.
The auditor said that the short and delayed release of subsidy created a vicious cycle whereby funds taken on interest for working capital further increase the claimable subsidy eventually leading to "avoidable" increase in the overall food subsidy burden,
"Moreoever, the risk management policy of FCI also did not sufficiently address the complex financial needs of the corporation," the CAG noted.
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