Boots has suspended payments using loyalty points in shops and online after attempts to break into customers’ accounts using stolen passwords.
Customers will not be able to use Boots Advantage Card points to pay for products while the issue is dealt with.
Boots said none of its own systems were compromised, but attackers had tried to access accounts using reused passwords from other sites.
It comes days after a similar issue hit 600,000 Tesco Clubcard holders.
A spokeswoman for Boots told the BBC the issue affected less than 1% of the company’s 14.4 million active Advantage Cards – fewer than 150,000 people.
But it could not give an exact number as the company was still dealing with the problem.