The average stamp duty bill for first-time buyers has almost doubled over the last five years, says a report from mortgage lender Halifax.
The average bill in 2007 was £1,751 compared with £960 in 2002.
In the south-east, south-west and east of England almost all first-time buyers paid stamp duty, while in northern regions only 42% were liable, it said.
The Treasury pointed out that half of first-time buyers will pay no stamp duty this year.
The lowest, 1% tax band hits homes worth between £125,000 and £250,000.
Homes valued between £250,000 and £500,000 attract a 3% charge and properties worth more than that are taxed at 4%.
Although the government has raised the threshold at which buyers pay 1%, it has not kept pace with the surge in house prices.
“Stamp duty has again become an issue for first-time buyers because the stamp duty thresholds have not kept pace with house price inflation,” said Martin Ellis, Halifax chief economist.
“We call on all political parties to raise the stamp duty thresholds to compensate for house price inflation over the past decade,” he added.
But the government defended its record.
“Half of all first-time homebuyers and around two-fifths of all homebuyers will pay no Stamp Duty Land Tax this year,” a Treasury spokesman said.
Meanwhile, the latest figures show that the UK housing market is slowing.
According to a monthly survey from the Halifax, prices across the UK fell by 0.3% in February, taking the annual rate of inflation down from 4.5% to 4.2%.