Civic leaders have questioned the accuracy of the national census, claiming they have "lost" a population the size of Arundel.
The anomaly was revealed as Arun District Council announced its provisional budget for the new financial year, which begins in April.
It shows residents in Littlehampton, Bognor and Arundel will see their council tax bills increase by 6.5 per cent.
The 2001 census figures showed there were about 3,000 fewer people living in the district than the council thought - about 141,000 compared to 144,000.
Council leader Norman Dingemans said this had meant the Government's grant to the council for next year had been cut but the Office of National Statistics says it is confident the census was accurate.
Mr Dingemans said from April the average rate for a Band D property will rise from £114.30 to £121.77.
Mr Dingemans said: "A 6.5 per cent increase is one of the lowest increases of any district council in the South-East.
"We have been able to do this because of our seven-year financial strategy, which means we do not have to go down the boom and bust path."
He said the council would also be using more than £2million from its reserves.
Like West Sussex County Council, which is warning of council tax rises of between 15 to 20 per cent, Arun says it has also been hit by the Government's transfer of resources from the South-East to the north.
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