An investigator appointed to look into concerns about the Post Office’s Horizon IT system in 2012 came to believe that he was “dealing with a cover-up” by the state-owned body, which made “various threats” against him, a public inquiry has heard.

Ian Henderson, a chartered accountant, and his colleague Ron Warmington, who ran Second Sight Investigations, were appointed in 2012 to review cases of post office operators after MPs raised concerns about possible miscarriages of justice involving the Post Office’s Horizon IT system. Second Sight’s fees were paid by the Post Office, which had agreed to cooperate with the investigation.

However, Henderson said that after the first year of investigation, he believed the Post Office “was constantly sabotaging our efforts” to seek the truth and used claims of legal professional privilege – a type of confidentiality which covers legal documents – “to justify withholding documents from us”.

Henderson told the inquiry that Paula Vennells, the then chief executive, “frequently and consistently attempted to steer Second Sight away from investigating potential miscarriages of justice”.

“When I first met Paula Vennells, she told me that POL [Post Office Ltd] was the nation’s most trusted brand with a history of over 400 years. As our work continued, I increasingly formed the view that because of this history, POL somehow felt it was above the law,” he said.

“We tried to go where the evidence took us, but increasingly we were finding evidence of questionable conduct by POL, some of which, in my opinion, was probably criminal,” Henderson added.

He said by February 2015 he no longer believed the Post Office was taking Second Sight’s concerns about the Horizon IT system seriously. “I felt we were dealing with a cover-up by POL and possibly a criminal conspiracy,” he said.

Henderson told the inquiry that, during a short-lived mediation scheme for post office operators set up in 2014, Chris Aujard, the acting head of legal at the Post Office, “warned me to be careful about what I said”.

Aujard had said the state-owned body “would not hesitate to take legal action against me” under a “draconian” non-disclosure agreement (NDA) which he had signed, Henderson said.

“I took this as a thinly veiled threat to bankrupt me if I continued causing trouble,” Henderson said in his witness statement. “I was concerned about the various threats that had been made to me by POL concerning alleged breaches of my NDA and my duties of confidentiality … The most likely threats appeared to be an action for defamation, breach of confidence or breach of contract.”

The inquiry heard that Henderson became concerned after reviewing the case file of Jo Hamilton, one of the most high-profile victims of the scandal, who had been charged with theft and false accounting by the Post Office.

Henderson said the Post Office’s decision to charge Hamilton did not seem to be supported by its own internal security report, and there was evidence that “potentially exculpatory material” had not been disclosed to her at trial or subsequently. “I regarded this as either professional misconduct or, potentially, criminal conduct,” he said.

Henderson said he believed that the Post Office eventually terminated Second Sight’s contract in March 2015 because the investigators were “getting too close to the truth”.

He added: “Our overriding duty was, in a phrase attributed to Alan Bates, to help ‘the skint little people’ who didn’t have a voice and had been so badly treated.”

Warmington, the co-director of Second Sight, told the inquiry that in 2014 he had described the Post Office as having the “worst corporate behaviour I have ever come across”.

He said Vennells appeared to have “conveyed an extraordinarily rosy summary” of Second Sight’s interim report to the board in July 2013.

He added: “I wish that I had demanded, rather than asked, to more frequently see Paula Vennells, but also, when I was doubting whether the truth was penetrating through to her and the board, I should have demanded to address POL’s full board.”

The public inquiry is examining the Post Office Horizon IT scandal and why the state-owned body hounded post office operators for more than a decade, alleging financial shortfalls in their branch accounts and criminally prosecuting hundreds of people. It has since emerged that these financial discrepancies were caused by IT bugs within the Post Office Horizon computer system.

The inquiry continues.