The Royal Mint had been asked to make new 50p pieces featuring the October 31 date on which the UK was due to leave and a message of "Peace, prosperity and friendship with all nations", the BBC reported on Friday.
The Queen approved the order of the coins with the design featuring the monarch's head and a standard inscription on one side and the special message and date on the other, was approved at a meeting of the Privy Council on October 8.
But the Treasury said the initiative had now been "paused".
Up to 10 million new coins were reportedly being made ready for the October 31 deadline, in a project championed by Chancellor Sajid Javid since he took office in July.
His predecessor Philip Hammond had planned a limited edition of about 10,000 commemorative 50p coins to be sold to collectors for 10 pounds each.
Under plans, three different types of 50p Brexit coins were to be made from gold, silver and cupro-nickel - a mixture of copper and nickel.
The gold coins were not intended to enter mass circulation. But the silver and cupro-nickel ones were set to become legal tender.
The UK was due to leave the EU at the end of the month but, amid continuing political deadlock in Parliament, the bloc agreed on Friday to further delay the UK's departure.
It is set to a make a decision on the length of the extension to the Brexit process next week.
( With inputs from IANS )