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The Duchy of Cornwall will "carefully consider" the Public Accounts Committee (PAC) calls for greater transparency in their tax affairs.
However, representatives for the Prince of Wales' estate denied they had an "unfair tax advantage" over other businesses.
The next woman to inherit the throne should bear the title "Duke of Cornwall", according to a group of MPs.
As part of their investigation into Prince Charles' portfolio of land, property and investments, the Public Accounts Committee said the Duchy of Cornwall's charter needed to come in line with changes to the law of succession.
An estate run by Prince Charles needs to modernise and provide "greater transparency", the chair of an influential committee of MPs has said.
Labour's Margaret Hodge, who heads up the Public Accounts Committee, wants the Treasury to investigate the Duchy of Cornwall to see if it has an "unfair advantage" over other businesses in its tax payments.
The Prince of Wales' portfolio of land, property and investments may have an "unfair advantage" over other enterprises because it does not have to pay some business taxes, an influential group of MPs has said.
The Public Accounts Committee (PAC) want the Treasury to investigate the Duchy of Cornwall to see if an "unlevel playing field" has emerged as it is exempt from corporation and capital gains taxes.
In a report, PAC called for a more robust investigation from HMRC: "The Treasury does not do enough to properly scrutinise the Duchy's finances. It relies on the Duchy to provide it with accurate information without carrying out its own independent checks."
The estate generated £28.8 million over the last financial year, which the Prince received £19 million of as income - an increase of 4% on the previous year.