An ex-Post Office investigator suggested the words "system failure" be deleted from a witness statement to prove the Horizon system was not to blame for supposed missing money.
Graham Ward made the suggestion about a Fujitsu engineer's statement in the case of Anglesey sub-postmaster Noel Thomas in 2006.
Mr Ward told colleagues that the reference could be "damaging".
Mr Thomas, 77, was later wrongly jailed after his books fell short by £48,000.
More than 700 branch managers were wrongly prosecuted after faulty software made it look like money was missing from their shops.
Mr Ward - who now works for the Metropolitan Police - told the inquiry into the scandal he apologised for the suggestion, and admitted it was "the opposite" of his duties "under the law and to the court, properly and fairly to investigate".
Mr Ward, said: "I appreciate how it looks now and I'm sorry, but it was not my intention for that to happen [by] removing the words 'system failure'."
A former security team casework manager and financial investigator, Mr Ward wrote to employees of Japanese company Fujitsu calling on them to challenge any allegations that their Horizon program might be at fault.
In the email shown to the Post Office Horizon IT Inquiry, Mr Ward told Fujitsu employees: "Given the allegations made by the postmasters, I'm sure you'll agree that it's very much in ourselves and Fujitsu's interest to challenge the allegations and provide evidence that the system is not to blame for the losses provided."
But he told the inquiry on Thursday: "I can see now with the benefit of hindsight that it was a very one-sided view.
"At the time, certainly in the security team in terms of criminal cases, there weren't any cases of Horizon integrity challenges or whatever.
"I just wanted to do the right thing by ensuring that we were able to show that the system was working correctly."
He said that he had used "a poor choice of words", adding: "But that's the view I had at the time - I was just trying to do the right thing, but I've got it wrong, haven't I."
In his witness statement, Mr Ward said it was not part of his role to review witness statements, and had annotated a draft statement by the Fujitsu engineer, Gareth Jenkins, because he was "trying to be helpful".
Asked by counsel to the inquiry Jason Beer KC why he had taken issue with Mr Jenkins' words "system failure", Mr Ward said: "I just think what I was really looking at was getting a full explanation of what Mr Jenkins was saying in his statement about what a system failure was, because it didn't appear to me to be terribly clear.
"I would not have said anything along the lines of 'you can't say this' or whatever, I was just trying to get some clarity."
Mr Thomas was jailed for nine months for false accounting in 2006, but had his conviction quashed in 2021.
The inquiry continues.