Whistleblower David Phelan claimed patients were removed from lists at Kettering General Hospital because national targets were being missed.
The hospital said it used data filtering to get a "true picture of the size of its waiting list" but the practice had stopped in December 2015.
It said its data management had been "well intended, if misguided".
It has not provided figures for the impact the filtering practice had on waiting lists.
The hospital denied it was trying to seek any "financial advantage" from its actions, which emerged following a BBC investigation.
It also acknowledged that a new system it implemented in March 2016 and dropped in May 2017 had been "flawed".
The system suggested 25,000 patients had been on the waiting list for more than 52 weeks, but following a validation process a year later it emerged that 283 patients had been waiting more than 52 weeks.
Of those patients, two experienced "moderate harm", which meant their condition had deteriorated, the hospital said, and 136 had experienced "low level harm", where their symptoms continued for longer.
The hospital's medical director Dr Andrew Chilton said: "Our systems and working practices were historically inadequate but have now been extensively reformed and brought up to date.
"Our historic handling of waiting times - while inadequate - was well-intentioned and there is no evidence of fraud whatsoever."
Former governor Mr Phelan, who stepped down in June, claimed the trust manipulated the figures to avoid being fined for patients waiting longer than 52 weeks.
The NHS regulator can fine trusts for breaches of waiting times per patient.
Dr Chilton said "data filtering" was used to remove patients who were not part of the dataset measured by national referral to treatment time pathways.
He said it was done so the hospital could establish the true size of its waiting list to plan resources and activity accordingly.
The hospital said it aimed to meet the 18-week NHS waiting list target by 2018.
A hospital accused of "fiddling" its waiting lists to meet targets has admitted it "filtered data".