The heir to the throne's estate, the Duchy of Cornwall, owns more than 53,000 hectares of land and has a financial portfolio.
Dating back to 1337, it was set up to provide an income for the monarch's oldest son and heir apparent, and currently has assets valued at 763 million pounds (USD 1.2 billion, 900 million euros).
As a public "crown" body, Charles' estate is exempt from capital gains and corporation tax, although he pays tax on his own income from the estate.
The Treasury relies on the duchy to provide it with accurate information on its finances, the MPs' report said, while Charles's own accounts also needed to be more transparent.
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The royal estate should also amend its charter to allow a female heir to inherit the duchy, in line with recent changes to succession law, the committee said.
"There are a number of steps that could help to bring the duchy, an historic institution, more in line with the expectations of the present day," said the committee's chairwoman Margaret Hodge.
"The Treasury should examine whether the duchy's tax exemption creates an unlevel playing field," she added.
A spokeswoman for the royal estate said: "We do not believe the duchy has an unfair tax advantage over its competitors... The duchy is not subject to corporation tax and the duchy is not a corporation.
"The duchy is exempt from tax on capital gains. Any capital gains have to be reinvested in the business and cannot be distributed."
The Treasury said it has a "constructive" relationship with Charles's estate and "challenges decisions where appropriate".