A former boss of the Post Office sent an email to two staff members in 2009 telling them his instinct about the Horizon scandal was that “subbies with their hand in the till” were blaming the technology, it has been revealed.

The message from Alan Cook, who was Paula Vennells’s predecessor, came to light at a session of the Post Office Horizon inquiry in central London.

In the email to Mary Fagan, a former corporate affairs director at Royal Mail, and a second employee, Cook described a “steadily building nervousness about the accuracy of the Horizon system” at a time when the press were “on it”.

He wrote: “My instincts tell that, in a recession, subbies with their hand in the till choose to blame the technology when they are found to be short of cash.”

Cook did ask for the claims about Horizon to be examined, although he admitted to the inquiry that he did not recall receiving the findings before leaving in January 2010.

He also said he was unaware until the very last months of his time leading the Post Office as managing director that the organisation was independently prosecuting branch operators. There were 160 prosecutions by the Post Office of branch operators during Cook’s tenure from March 2006 to January 2010.

When asked how it was that the Post Office was spending hundreds of thousands of pounds in legal costs pursuing branch operators over comparatively small sums, Cook said he believed the decision had been made by Vennells, who was then network director. She later replaced him in leading the organisation.

Asked about his comments in the email, Cook told the inquiry: “It’s an expression I will regret for the rest of my life. It was an inappropriate thing to put in an email and not in line with my view of subpostmasters.” He said he should have known and done more.

Between 1999 and 2015, hundreds of post office operators were accused of negligence and in some cases convicted of crimes relating to theft, false accounting and fraud, based on faulty information from the Horizon computer system, which erroneously suggested that money had gone missing from branch accounts.

Sam Stein, a lawyer representing some of the post office branch operators, raised the case of a client, Janet Skinner, now 52, who was given a nine-month prison sentence in 2007 over an alleged shortfall of £59,000 from her post office branch in Bransholme, Hull.

She had made more than 100 calls to a helpline to seek help but felt put under pressure to plead guilty in court in order to reduce her potential sentence.

“I did not appreciate what was going on,” Cook said. “When I had reports about them and the individual who pleaded guilty, then I thought we must have been in the right.”

Cook apologised to Skinner in the inquiry room. Speaking later, Skinner told reporters: “Probably he is being sincere, but I think his evidence has been insincere. He was sat at the head of that table and he would have known what was going on.”

The inquiry also heard from Adam Crozier who was chief executive of Royal Mail Group Ltd from 2003-2010, a period during which the Post Office was part of the organisation.

Crozier said he, too, had not known that the Post Office through Royal Mail lawyers was prosecuting branch operators, although he found it “surprising” to hear that Cook was also ignorant. He said: “He certainly always gave the impression of someone who was very much in control of his brief.”

Crozier said the Post Office had operational independence and that he did not recall being told about problems with the Horizon system.

He said he did not understand why the Post Office had not commissioned an “independent view” of the IT system when its issues became clear.

“I can see that there was a lack of transparency now in the Post Office,” he told the inquiry. “I had assumed they were making the same strides that we were in the rest of the company.”

Crozier left Royal Mail to become chief executive of ITV. He did not feature in the channel’s drama Mr Bates vs the Post Office about the scandal.