The news is a further setback to a college beset with difficulties in recent years. Not least of those is the pending court appearance of a former employee.
Roy Colin Ackerley is accused of false accounting and furnishing false information, charges relating to applications for European Union contracts while he was a co-director of the Wight Management Agency, a division of the college.
The college has also seen a succession of principals - three in 18 months.
The latest financial figures for the year to July 1999, show that over the previous two years the college had paid back more than pound;500,000 to the European Social Fund for income claimed for students not enrolled at the college - a situation unconnected with the charges relating to Mr Ackerley.
In a statement the college management said that the pound;647,000 loss, which does not take account of depreciation, was of great concern. It is now putting in place measures to achieve a significant reduction in its operating costs following talks with the Further Education Funding Council.
Already the current principal, John Parnham, with the backing of the governing body, has drawn up plans to freeze budgets and cut costs.
Staff have been told likely meaures include: review of staffing; a further round of management restructuring; review of contracts of employment; review of services provided externally; and funding cost-of-living pay increases from efficiency gains.
The report and financial statement for 1998-99 also confirm that previous principal Dr Michael Taylor was given a pound;30,000 pay off.
This is described as compensation for loss of office, although at the time the college maintained Dr Taylor had left his pound;57,371 post by mutual consent.
The amount of payback to the European Social Fund totals pound;519,000 so far, with a warning that this is only an estimate.
The deficit of pound;647,000 compares to the overspend in 1997-98 of pound;445,000, but much of this is due to one-off payments in connection with restructuring.
The college is currently undergoing changes with new governors appointed and specialist staff recruited since Mr Parnham took office in September 1999.
It hopes to break even in 2000-1 and to have a surplus by 2002. But it has appealed to islanders to use the college or lose it.
Its statement said: "It is for the island's students, parents, schools, businesses and employers to recognise the college's importance to the island community, and, if they can, support their local college in its steady recovery."
NATFHE, the lecturers' union, said it would be consulting with Mr Parnham.