The UK Charity Commission is investigating allegations that the fund has been channelling money to militant group Hamas.
Treasury officials claim the London-based fund has been a major route used to hide the flow of money to Hamas.
It is understood that the charity will still have access to its money to fund its work, but all transactions will have to be approved by the commission while it conducts its enquiries.
The charitable fund, also known as Interpal, raises £2m to £3m a year, meant for relief efforts in Gaza, Lebanon, Jordan, and the West Bank.
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