A £50m budget shortfall will see about 90 jobs being cut at the South East England Development Agency (Seeda).
The agency is being restructured and the full extent of job losses will become known by April 2010.
A Seeda spokesman said it was looking at a potential figure of 90 job losses, but it could be more or less.
Cuts will be made through a voluntary scheme, restricting external recruitment and cutting down the costs of hiring temporary staff.
The government funded agency represents the counties of Berkshire, Buckinghamshire, Hampshire, the Isle of Wight, Kent, Oxfordshire, Surrey and East and West Sussex.
It was set up in 1999 to boost the economic regeneration of the South East and currently has 370 staff.
In a statement Seeda said the economic downturn had had a "significant impact" on its financial resources.
"Funding for Regional Development Agencies has been redirected towards measures to help businesses and home-buyers survive the downturn and our budgets are reduced further as we will not now earn expected capital receipts from sale of land and properties.
"As a result, we have about £50m less than we expected to invest in our programmes over the next two years.
"Over the next two years we also need to save £3.6m from our administration budget. Whilst we will reduce overheads where possible, these will mainly be taken from staff savings."
Seeda said it was predicting about 90 potential job losses affecting its offices in Guildford and Chatham, but the exact number and location of the cuts would only be known following the completion of its restructuring programme by April next year.
Cuts will be made through a voluntary early release scheme to be launched next month, restrictions on external recruitment and reducing temporary and interim staff costs.
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