The chief executive of the Post Office, Nick Read, will return part of his £450,000 bonus for last year, after a rebuke from the chairman of the inquiry into the Horizon computer scandal.
In its financial accounts for last year the Post Office said its executives had met all their obligations to support the inquiry into the system.
But the inquiry is still taking place.
They also wrongly said inquiry chairman Sir Wyn Williams had approved bonuses relating to that support.
Mr Read apologised for what he described as "unacceptable errors".
In a letter to the inquiry chairman, Mr Read admitted the firm had made an "incorrect statement" in its accounts.
The Horizon inquiry is investigating how hundreds of sub-postmasters became victims of a vast miscarriage of justice.
They were blamed for discrepancies in their sub-post office's finances and prosecuted, with many receiving prison sentences, criminal records or going bankrupt. The discrepancies were down to the Post Office's glitch-prone IT system, called Horizon.
In the Post Office's annual accounts for last year published on 1 March, there was a target for executives defined as: "All required evidence and information supplied on time, with confirmation from Sir Wyn Williams and team that Post Office's performance supported and enabled the Inquiry to finish in line with expectations".
The metric was marked as '"achieved" although at the time the bonuses were agreed the inquiry was still in its first phase. It is likely to continue until 2024.
After a lawyer acting on behalf of Sir Wyn questioned the accounts, the Post Office issued a statement apologising for the "inappropriate sub-metric related to the Horizon IT Inquiry".
In a letter addressed personally to Sir Wyn, Mr Read apologised and said he would return the remuneration associated with that sub-metric.
The Post Office board is considering whether other members of the leadership should do the same.
The inquiry has heard moving testimony from dozens of sub-postmasters who were falsely accused of fraud. Hundreds lost their livelihoods, were stigmatised in their communities, and some sent to prison.
Dozens of convictions have now been overturned in the courts, but many of those wrongly convicted are still awaiting compensation.
The next phase of the inquiry due to start next month will look at the action taken against the sub-postmasters, and knowledge of and responsibility for failures in investigation. A later phase will explore governance including whistleblowing over the scandal.
Mr Read said in his letter that he regretted the errors made particularly against the background of "deeply concerning" evidence presented to the inquiry.
He added: "Our clear intent remains to offer full and fair compensation as quickly as possible and we are doing all we can to work with the government to achieve that."