A review commissioned by the Government into a troubled £178m IT system for paying farmers considered scrapping the scheme.

The secret report by Fujitsu, leaked to the Herald, was judged to be so sensitive that MSPs were told not to circulate it.

However, while the probe did not recommend abandoning the system, areas were flagged up as being “sub optimal” and “poor quality”.

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The £178 million programme, which closed at the end of March, was supposed to reform Common Agricultural Policy payments.

Cconfidence in the scheme suffered a blow after payments to hundreds of farmers were either delayed or missed.

In a report last week, Audit Scotland warned that the Government could face fines of up to £60m due to the problems.

It has now emerged the Government tasked Fujitsu, a Japanese IT giant, with carrying out a ‘technical assessment’ of the project.

MSPs on two Holyrood committees were given sight of the report, but the Government did not publish it on the grounds of commercial sensitivity.

According to the independent report, obtained by this newspaper, the architecture behind the IT system is “fundamentally sound”, but the design documentation was of “poor quality and incomplete”.

The report noted there was a “substantive risk to future system stability”, adding: “Acceptance of an environment in which documentation is not created or kept up to date has been allowed to persist. This must stop.”

In another section, Fujitsu concluded that quality had been compromised in “many areas” in order to “expedite delivery”.

The review also claimed “insufficient” business resource had been ploughed into “analysis and testing”.

In addition, the analysis, design and development teams were judged to have been of a “lower quality” than “we have seen elsewhere”.

Five options for reform were considered, including scrapping the current system and replacing it with a bespoke re-write.

However, Fujitsu estimated this would cost up to £40m and carried a “high” risk.

The second option was to scrap the scheme and procure a “packaged solution replacement”, but again the company slapped a “high” risk warning on this outcome.

Other options were considered, but the “most appropriate course of action” was improving governance, environmental management, analysis and design:

“In other words, strengthening core capabilities that are, largely technology independent.”

On May 10th, a senior civil servant told the Rural Economy and Connectivity Committee why she believed the report should not be published:

“Something that would worry me about making the information more public, certainly at this stage and possibly over a longer period, is that the report’s authors reveal vulnerabilities in the IT system, which potentially leave it vulnerable to cyber attack, which would obviously be unacceptable.”

However, in a letter to SNP Cabinet Secretary Fergus Ewing eight days later, the Public Audit and Post-legislative Scrutiny committee expressed its dismay at the secrecy:

“We appreciate that there will very occasionally be circumstances in which issues of commercial confidentiality mean that a document relevant to the public sector cannot be published. In this case, however, no explanation was initially provided as to what made the report commercially sensitive.

“I do not consider this situation to be acceptable, particularly in relation to a multimillion public project that has been beset by problems and delays, and which has caused considerable difficulties for farmers, crofters and rural communities.”

Scottish Tory MSP Finlay Carson said: “This is a report which is severely critical of the Scottish Government’s role in the CAP crisis, which is exactly why the SNP doesn’t want to make it public.

“But for the sake of Scotland’s rural communities, who were starved of hundreds of millions of pounds as a result of this fiasco, it has to be published."

A Scottish Government spokesman said:

“The Fujitsu review concluded that the system is architecturally sound and should be retained. Its purpose was to verify that the technical environment that is in place, and the processes that are established to maintain and enhance it, are sustainable for current and future needs, and are in line with industry standards. The review report was balanced in that it acknowledged improvements that had already been made while identifying what more we should do to improve the system.

A spokesman for Fujitsu said: “Fujitsu is not making any additional comment on the report.”