The health authority for Sussex and Surrey faces a deficit of nearly £40m, according to a report.
The review by the Liberal Democrats said 19 of the 28 health authorities across England faced debts totalling £400m for the 2002 to 2003 tax year.
Of these, the Surrey and Sussex Healthcare NHS Trust has the third largest budget shortfall at £39.6m, according to the party's calculations.
Liberal Democrat health spokesman Dr Evan Harris blamed a lack of government funding for the Surrey and Sussex authority's huge debts.
High cost of living
He said hospitals were being forced to go into the red in order to employ temporary staff and maintain stocks of expensive drugs.
But the Surrey and Sussex Healthcare NHS Trust said progress was being made in controlling the amount of money spent.
It issued a statement saying it was on course to reduce its overall shortfall from £68.4m to £25m in the year to come.
"Over the past year there has been significant progress in addressing the historic financial problems," the trust said.
"There is real emphasis being placed on achieving sustainable financial balance as well as providing high quality, safe services, and the progress over the past year is encouraging."
Reasons for the shortfall included the relatively high cost of living in the South East and high levels of employment, which led to a reliance on agency staff, the authority said.