David Phelan, a Kettering General Hospital Trust governor, said patients were removed from lists because national targets were being missed.
The governors were due to look at a resolution claiming his behaviour had breached its code of conduct.
But Mr Phelan decided to resign from his position as a governor.
The governors had stressed the decision to take action against him was not connected to his whistleblowing.
Kettering General Hospital's lead governor Stuart Lake said the governors had backed a resolution saying the Mr Phelan had committed a "serious breach of the trust's code of conduct" due to "hostile, abusive and disruptive behaviour".
He said Mr Phelan had decided to leave the meeting before presenting his case.
Mr Phelan said he believed the action of governors was connected to him whistleblowing.
"I believe the truth will out," he said.
In May, a BBC investigation found thousands of Kettering General Hospital patients had waited a year or more for operations.
The hospital admitted there had been "anomalies" and that a thorough review of data had been carried out.
A hospital review has found that 138 patients were harmed - including one who had substantial sight loss - as a result of the long waits.
Mr Phelan, who raised concerns under whistleblowing procedures, was working as associate general manager in the trauma and orthopaedics department when he discovered discrepancies in the referral to treatment time (RTT) data in October 2015.
He warned managers that the daily RTT report was understating the true position by half when checked against patient records.
He told the BBC he discovered managers at Kettering General Hospital had used six exclusion categories to remove patients from their official waiting list data.
The NHS regulator fines for breaches of waiting times are per patient.
A hospital spokesman said: "We suspended reporting of our waiting list data to the Department of Health in December 2015 when we became aware of some anomalies which suggested there could be some issues with our systems."
The hospital said it was confident the issue had been addressed.
A whistleblower who alleged that patients were removed from a hospital's waiting lists to "fiddle" the system has resigned as a governor.