Concerns about East Suffolk and West Suffolk Primary Care Trust's combined overspend of more than £30m have been highlighted by the Audit Commission.
Plans to save cash by closing hospitals have been criticised
An audit report says the two PCTs are still facing major financial problems.
"There are financial recovery plans in place for future years, but there is a risk that the savings forecast in those plans will not be achieved," it says.
East Suffolk PCT and West Suffolk PCT said progress has been made on budgets.
The report found that the PCTs had overspent their budgets in 2004/05: Suffolk East by £20.1m and Suffolk West by £12.5m.
Based on current plans, in 2005/06 Suffolk East is forecasting a deficit of £19.8m and Suffolk West a deficit of £13.8m, it says.
'Tough financial climate'
Robert Davies, the District Auditor, said: "Despite the challenging task facing them, the PCT Boards and management teams are committed to the delivery of their financial savings plans and significant savings have already been reported.
"However, they need to continue to work with Norfolk, Suffolk and Cambridgeshire Strategic Health Authority and with other stakeholders in the local health economy to achieve further planned savings."
Tony Robinson, chair of Suffolk East Primary Care Trusts said: "It is a very tough financial climate for us but we are in much better shape now than we were 12 months ago.
"We welcome the report and thank the Audit Commission for their insight into our financial standing. The Boards are determined to continue this progress and to achieve both financial health and better services for patients."
A spokesman for West Suffolk PCT said the Trust had "agreed a financial recovery plan in July last year - two months after Mike Stonard became the PCT's new Chief Executive - the PCT's financial position has improved continuously".
He said: "In December last year, a 'turnaround team' from management consultants KPMG, commissioned by the Department of Health, gave Suffolk West PCT a clean bill of health for its financial and general management."