People should pay the right amount of tax. But HMRC does not always ask for the right amount," said committee chairman Andrew Tyrie.
"Some taxpayers may find money taken from their accounts that later should be paid back. That would be unacceptable."
He said the committee also had "deep reservations" about changes to tax policy that would require upfront payment of any disputed tax associated with tax avoidance schemes.
"Retrospection should be considered only in wholly exceptional circumstances. The latest measure would have to be justified on those grounds," Mr Tyrie said.
"Retrospection puts policy on a slippery path to arbitrary taxation, discouraging investment and innovation and creating the scope for great unfairness."
Committee member Mark Garnier, a Conservative MP, said at the moment HMRC needed a court order to be able to seize money from accounts.
The committee is concerned that the current system of checks and balances could be upset.