He said Ajit's resignation on "emotional grounds" diverted the "focus" from the Pawar senior's move which would have otherwise given a much-needed political leverage to the NCP in the run-up to crucial elections.
Ajit had told a news channel that "obstinacy" of some NCP leaders had led to the arrest of Shiv Sena supremo Bal Thackeray in 2000, which he said was a "mistake".
Ajit didn't take name of Bhujbal, a former Shiv Sainik, who was Home Minister in the Congress-NCP government that time.
Speaking to a news channel, Bhujbal said he never intended to "trouble" the Sena founder.
"The issue of arresting Bal Thackeray had ended that time only. I had just signed a file on the (1993) Mumbai riots prepared by the Shrikrishna Commission. I had filed a case of defamation (against Thackeray) after a report in 'Saamana' on desecration of B R Ambedkar's statue despite I being given a clean chit in the matter earlier," he said.
"I withdrew the case later. After that I was invited to 'Matoshree' by Balasaheb and Uddhav Thackeray. I went there with my family members and spent around three-four hours there," Bhujbal said.
On the abrupt resignation by Ajit, nephew of Sharad Pawar, Bhujbal said the former could have waited for two more days before quitting as the MLA.
"What was the compelling need to resign on the day (September 27) when Pawar had announced that he would visit the ED office in Mumbai. He (Ajit) says he is an emotional person. But he could have controlled his emotions for two more days. There was groundswell of support for Sharad Pawar on that day, but his (Ajit's) act shifted the focus of the day...I wonder who benefitted from this," Bhujbal said.
The sudden resignation of Ajit had triggered speculation of a rift in the Pawar clan.
Later, Ajit clarified that he resigned because he was "pained" to see that his uncle was being "falsely implicated" in the Maharashtra State Cooperative (MSC) Bank scam case "because of him".
The ED had registered a case against Ajit, Sharad Pawar and others in connection with the alleged scam.
Bhujbal, currently out on the bail in a money laundering case, is the NCP nominee from Yeola assemblysegment in Nashik district.