Pawar had caused a flutter with his remarks that he didn't think that people have doubts about Modi's intentions in the purchase of fighter jets from France.
Objecting to Pawar's remark, NCP founder member Tariq Anwar and general secretary Munaf Hakim had quit the party last week.
The statement had come at a time when the Congress has launched a pointed attack on the prime minister over the deal and is trying to forge an alliance with the NCP for future polls.
"Some people have criticised me saying I supported him (Modi). I have not supported him. I did not (support Modi) and will never (do that)," Pawar said while addressing a party meeting here in the Marathwada region.
He said, "They (the government) bought the aircraft. I am saying this clearly that the government should explain it to Parliament why the cost of the aircraft rose from Rs 650 crore (per plane) to Rs 1600 crore".
Pawar's recent comments which was inferred as defence of Modi was welcomed by the BJP and party president Amit Shah had thanked Pawar for the same.
However, the NCP had claimed that Pawar was quoted out of context by the media.
The NCP chief Monday reiterated the demand for a probe by a Joint Parliamentary Committee (JPC) into the Rafale deal and demanded the government share details of the prices of the 36 fighter jets.
The former Defence Minister also said that there was no need to make public the technical details relating to the aircraft.
Pawar, who served as Agriculture Minister under the erstwhile Manmohan Singh government, also hit out at the Central and Maharashtra governments over agrarian issues.
He hailed the previous UPA government's decision to write off farm loans worth Rs 71,000 crore.