DEFRA secretary Caroline Spelman faces further scrutiny after it emerged that her husband helps run the company in charge of the £350m computer system at the Rural Payments Agency.

Mark Spelman is a managing director at Accenture, the firm that developed the online system that delivers subsidy payments to farmers.

The revelation comes just days after questions were raised over Mrs Spelman’s past involvement with her husband’s biotech lobbying company.

The Rural Payments Agency (RPA) awarded Accenture a £35m seven-year contract to develop new and more efficient systems in 2003.

Accenture was appointed to develop and deliver the new system over two years and then provide ongoing support for the remaining five years.

The agreement – made long before Mrs Spelman was appointed DEFRA secretary and while the Tories were in opposition – is due to expire this year.

But Mrs Spelman now finds herself in charge of the government department that will ultimately decide whether Accenture’s contract should be terminated.

Although the Accenture contract was initially worth £35m, the cost of the IT system spiralled to £350m over the next few years.

In one of its most damning reports ever, the government’s public spending watchdog last year called for the system to be scrapped.

“The IT system does not meet the scheme’s needs,” said the National Audit Office document published last autumn.

More than 100 Accenture contractors were employed at the agency at an average cost of over £200,000 each in 2008-09, the report revealed.

“Without any alternative system to fall back upon, the agency appears to have little choice but to continue with the existing IT systems in the short term.”

This spring, then DEFRA secretary Hilary Benn ordered the RPA to cut costs and improve the service it gave to farmers.

Targets included reducing administration costs by 10%, paying more subsidies on time and reducing the cost to the taxpayer for each application.

The RPA business plan for 2010/11 states that the agency will review and change its processes, structures and IT systems to meet customer needs.

The Conservative Party website states that Mrs Spelman met her husband Mark, a partner at Accenture, while living in Paris.