It said that a "small number of coins" were affected when they were struck at a rapid rate during production.
The Royal Mint is striking 1.5 billion new 12-sided one pound coins, introduced to help crack down on counterfeiting.
Out of shape versions of the coin, considered collectors' items, are appearing on Internet auction sites.
The Sun newspaper has spoken to a number of people reporting warped coins, although doubts have been raised about the cause of reported highly-damaged coins.
Also Read
"As you would expect, we have tight quality controls in place, however variances will always occur in a small number of coins, particularly in the striking process, due to the high volumes and speed of production."
The Mint has claimed the new one pound coin is the "most secure coin in the world", replacing the previous one, of which about one in 40 are thought to be fake.
He said that if the middle of the two-piece one pound coin was missing, it would not get through the quality checks.
The new coin has a string of anti-counterfeiting details, including material inside the coin itself which can be detected when electronically scanned by coin-counting or payment machines.
Other security measures include an image that works like a hologram, and micro-sized lettering inside both rims.
It is not the first currency launch in the UK to have hit problems in recent months.
Disclaimer: No Business Standard Journalist was involved in creation of this content