ISoft delayed its results earlier this year after reports of accounting errors and its auditor, Deloitte, said it was unable to state whether the accounts just published gave a true position of the firm's financial position.
New rules
The company reported a £343.8m pre-tax loss in the year to 30 April, mainly as a result of writing down the value of Torex, a company that iSoft bought in 2004.
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Long-term shareholders will be feeling deeply disappointed by the events of recent months
John Weston, iSoft acting chief executive
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ISoft's results - which saw sales rise 8% to £201.7m - were reported under a new accounting policy after the firm admitted earlier this year that it had found evidence of irregularities affecting its 2004 and 2005 accounts.
The problems - now being investigated by the Financial Services Authority (FSA) - mainly relate to the firm's revenues being stated earlier than they should have been.
A previous independent probe into iSoft's accounting problems also concluded there were grounds for a more formal investigation and resulted in the suspension of commercial director Steve Graham.
Troubled project
The firm has been blamed for delays to the 10 year multibillion upgrade of the NHS computer system.
It is supplying software to health trusts in the Midlands and north of England which will operate a new national electronic patients register.
The National Audit Office warned in June that the huge project faced "significant challenges" if it was to be delivered on time and budget.
ISoft has been accused of breach of contract by Accenture and CSC, the two firms overseeing the project, which it denies.
Acting chief executive John Weston said the last year had been a "turbulent" one and that a stream of negative publicity had damaged the firm's reputation and customers' willingness to sign contracts with it.
"Long-term shareholders will be feeling deeply disappointed by the events of recent months," he said.
"I share that disappointment but I am determined to see through a series of actions and change that I believe are necessary to put this company back on a solid footing."
Political pressure
On Wednesday, growing concern about the health of iSoft prompted MPs to demand that the Department of Trade and Industry also investigate the company.
The FSA's inquiry is the latest in a long line of problems to hit the group. In June, its chief executive Tim Whiston resigned while another employee has been put on a leave of absence.
Announcing its results, iSoft said it was unable to predict at this stage what its revenues would be in the current year.
It also said it was likely to cut at least 150 jobs, equivalent to 15% of its UK workforce, as it tries to reduce costs.
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