Fadnavis said his dispensation took the decision in view of "the big scam" which occurred in Maharashtra after the then UPA government at the Centre wrote off debts in 2008, which, he said, deprived distressed peasants of the benefits intended for them.
The Maharashtra CM said the state government had formed a joint committee which would work out within a week conditions to ensure who should benefit from the waiver.
He suggested that farmers who were financially better off and professionals and government employees also into farming be left out of the scheme.
Fadnavis observed the waiver — announced on June 11 after a widespread farmers' agitation — would further stress the debt-ridden state, as his government would require raising Rs 25,000 crore or more for this.
"But it can be managed," he said at a recent interaction organised by BJP's 'Good Governance' department here.
He said implementing the relief measure would "take some time" and added the government might create "some financing instrument" to tackle the situation after the waiver.
Fadnavis also said decisions by Andhra Pradesh, Telangana and Uttar Pradesh to waive farmers' loans in their states led Maharashtra peasants to demand similar relief, which prompted his dispensation to announce the waiver.
He ruled out speculation that the move would cause prices to rise in the state and elsewhere.
"There was a big scam when loans were waived in 2008 in Maharashtra. The CAG (Comptroller and Auditor General) gave a very critical report on it, noting small farmers had not benefited, while the big ones looted money. So our biggest challenge now is to avoid such cases," he said.
Only farmers who needed the relief should benefit from it, he stressed.
Fadnavis praised his Andhra Pradesh counterpart, N Chandrababu Naidu, for doing a "good job" in using a digital platform to eliminate duplication of bank accounts after the AP government wrote off farmers' debts in the southern state.
"We are thinking of adopting such model. A decision will be taken at a cabinet meeting this month," he added.
Fadnavis, however, stressed that loan waiver was "not the ultimate solution" to end the miseries of farmers. Ensuring capital investment in the agriculture sector was a "challenge" before his government, he said.
The government was constructing one lakh farm ponds, digging as many wells and had embraced drip irrigation as part of such investments, he said, adding that the state government had invested Rs 25,000 crore in the agriculture sector.
"The challenge will be to keep doing this on a sustained level notwithstanding the loan waiver," he said.
To a question, Fadnavis said "some" political parties tried to spread violence from behind the scene when the farmers' stir was on.
"If you look at the FIRs filed in places where violence was reported (during the stir), it is not the farmers, but political leaders who have been named," he said.