The minister said the "significant" number of accounts should be audited to get better picture.
Pawar, however, did not rule out some possibility of exclusion of eligible farmers and inclusion of non-eligible farmers in the beneficiary list prepared by banks.
The CAG in a report tabled in Parliament on Tuesday found a number of shortcomings like ineligible beneficiaries getting benefit of the scheme while those eligible being denied. The CAG report was seized by Opposition Bharatiya Janata Party to attack the government alleging a Rs 10,000 crore scam in the 2008 debt waiver scheme.
"Government of India has taken the decision and money has been sent to banks. Accounts and beneficiary list has been selected by banks under the supervision of RBI and NABARD. Money has directly been transfered to accounts. Where is the question of misappropriation?" Pawar told reporters here.
"We have to understand out of 3.7 crore accounts, CAG has taken sample of 90,576 accounts. That means 0.25 per cent accounts have been audited. With such a big scheme announced throughout India, coming to conclusion with such small figure! I think I should get more information," Pawar said.
He said the issue should be discussed "when significant number of accounts are audited, that will give better result."
After receiving the preliminary report of CAG, the Union finance ministry had written to RBI and NABARD that the number of accounts taken for auditing by CAG was not "sufficient" and all accounts should be audited as early as possible, he added.
"If suppose those people are not eligible but have got advantage, I am sure banks will recover that money. There are certain farmers, who are eligible but not got advantage. As on today, there is no budgetary allocation but we have to apply our mind. We have to take some view after getting the report."
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