Thousands of post office operators have complained they continue to suffer problems with the system at the heart of the Horizon IT scandal, with nearly all involving a financial shortfall.

As the final phase of the inquiry into the Post Office Horizon IT scandal began, the results of a damning survey shows operators are still struggling with bugs in the system, that trust in the organisation is low and that they believe compensation should be higher.

Almost 98% of post office operators who participated in a survey as part of the inquiry into the IT scandal who continue to encounter “discrepancies” with the system have said the issue involved a financial shortfall.

Nearly 70% of the respondents to two anonymous surveys, which were sent to 16,000 post office operators before the start of the final phase of the live inquiry, which starts on Monday, said they had experienced an “unexplained discrepancy” on the Fujitsu-built IT system since January 2020.

Of those, 35% have encountered problems as frequently as a few times a month, with 18% citing problems once a month.

The public inquiry is examining the Post Office Horizon IT scandal, in which 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’s Horizon computer system. While 98% said they had encountered shortfalls, 34% also said the IT system produced surpluses in their accounts.

When asked how these discrepancies were typically resolved, almost three-quarters of respondents said they had to use either their branch’s money or their own to resolve the mis-balance.

Overall, 92% of post office operators said they had experienced some form of glitch with the Horizon IT system in the past year.

The most common form of glitch in the system, for which Fujitsu has a £2.5bn lifetime contract, took the form of screen freezes or loss of connection.

Almost half of respondents said they were dissatisfied with their role as a subpostmaster – although 31% said they were satisfied – with 72% saying they felt “undervalued” by the Post Office.

Just over half felt the state-owned organisation was not trying to improve its relationship with post office operators.

More than 68% disagreed that the Post Office was professionally managed, 65% said it was not a trustworthy organisation, and 55% disagreed with the statement that it had learned lessons from the Horizon IT scandal.

The second survey looked at the performance of the Post Office in relation to the various compensation schemes set up in the wake of the scandal that led to more than 900 operators being wrongly prosecuted due to bugs in the Horizon system.

Just under half said they were dissatisfied with the Horizon Shortfall Scheme, while 47% of respondents said it was hard to understand.

“There was a sense that the process was too long, with a lack of transparency – for example, the cause of certain delays or information about how cases were progressing,” the YouGov survey said. “Some applicants surveyed believed that the amount of compensation received or offered was not sufficient, in particular to compensate for additional stress caused.”

Last week, it emerged that Nick Read, the embattled chief executive of the Post Office who is due to give evidence to the inquiry next month, is to step down next year.

The final phase of the inquiry, which is being chaired by the former high court judge Sir Wyn Williams, is looking into the practices and culture of the Post Office, and its delivery of compensation to wrongfully prosecuted post office operators.

As part of a move to repair relations and improve oversight, the Post Office appointed two operators as non-executive directors for the first time in 2021.

The directors, Saf Ismail and Elliot Jacobs, will give testimony over the first two days of the inquiry this week.

The inquiry will also delve into the strained relations between the Post Office and the government when the organisation’s former chair, Henry Staunton, appears early next month.

In January, Staunton was sacked by the then business secretary Kemi Badenoch, and went on to accuse the government of wanting to delay compensation for post office operators until after the general election.

Badenoch is due to appear in early November, on the same day as Kevin Hollinrake, the former Post Office minister who helped push through unprecedented legislation allowing more than 900 operators to have their convictions overturned after being wrongfully prosecuted.

The final phase of the inquiry, in which more than 30 witnesses will testify, is due to finish in mid-November with two days of evidence from governance experts.