Six of these 40 PCTs are predicting they will dip further into the red over the financial year.
Cumbria, Leicestershire County and Rutland, Enfield, Buckingham, North Somerset and Wiltshire PCTs will all end 2007/8 with increased deficits - between them they will be £100 million further in debt than at the end of 2006/7.
A DoH quarterly financial report published last week forecast an overall surplus for the year of almost £1 billion, and said the total deficit of all NHS trusts was just £204 million. But these figures are based on performance in 2007/8 in isolation.
GP leaders criticised the presentation of the statistics as 'political spin' and urged the DoH to present data honestly.
GPC deputy chairman Dr Richard Vautrey said: 'I think there's some creative accounting going on in the NHS, as ever.
'Long-term debts are still a reality for PCTs and this has blighted local planning. The inherent debt hasn't gone away - the report is political spinning.'
Dr Vautrey urged the DoH to be 'more honest' to help patients understand why trusts are cutting services at a local level.
Hillingdon PCT, north-west London, one of the most debt-ridden trusts in the country with a deficit of £52.1 million at the end of 2006/7, confirmed that its deficit will be unchanged at the end of 2007/8.
PCT deputy director of finance Colin Peel said: 'We will carry forward our deficit of £52.1 million at the end of the year.
'We have agreed a programme with NHS London to pay back that deficit over the next four years, from 2008/9 to 2011/12.'
DoH claims in the report ignore historic deficits rolled forward from last year.
BMA chairman Dr Hamish Meldrum said the picture was 'not as rosy' as the one the DoH had sought to paint. A DoH spokeswoman said the figures show what trusts expect to achieve this year, managing within their resources for 2007/8.
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