He said the government will release the funds to those districts where the DCC Banks have submitted the complete list of eligible farmers.
Some DCC banks which have branches across many districts are yet to send complete lists of the loan waiver beneficiaries to the government.
Responding to a query on the opposition's criticism that farmers are being charged for submitting online farms for the loan waiver scheme, Phundkar said had that been the case, the administration would not have received about 55 lakh applications.
When told that some eligible farmers are being unable to apply due to problems in giving their thumb impressions, the minister said such cases will be considered eligible for the loan waiver in its next phase.
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Bowing to protests by farmers, the state government in June had announced a Rs 34,000 crore loan waiver with caveats. Under the scheme, loans up to Rs 1.5 lakh per farmer will be waived.
When asked about recent deaths of farm labourers in Yavatmal district due to spraying of pesticides on cotton crops, Phundkar said Chief Minister Devendra Fadnavis today approved a probe under Additional Chief Secretary (Home).
Although the government did not specify the number of deaths, eminent farm activist from Vidarbha, Kishor Tiwari, and the Shiv Sena said the pesticide exposure reported in Yavatmal district has claimed 18 lives so far.
Phundkar said neither the concerned district collector nor the local police are aware of these cases.
Announcing that the government will decide on banning the imported Chinese-make pesticide spray pumps, Phundkar said the cotton crops have grown to the height of almost six feet this year.
"The contract farm labourers have to spray the pesticide from a certain height. However, due to extreme heat conditions the labourers wear only vests and no other protective gear like face masks," he said.
"Agriculture department officials are now visiting fields to educate the labourers on wearing protective face masks and body wear," the minister said.
He said the probe will find out whether the Agriculture Assistance Centers which supplied the pesticides had briefed the farmers on the precautions to be taken while spraying the pesticides.
"There are reports are that some hospitals had handed over prescriptions to the relatives of the patients to get medicines from outside chemists and also get blood tests done from outside pathology laboratories. The probe will also find out why the affected patients were sent all the way to Nagpur, when Yavatmal has its own district hospital," Phundkar said, adding that the CM has already announced the compensation of Rs 2 lakh to the kin of the deceased and free treatment to those admitted in hospitals.