The 100ml tubes, labelled Colgate Cavity Protection, have been bought by thousands of customers at Sainsbury's and Boots stores.
The chains have sent warnings to customers who used loyalty cards for the purchase, but many others cannot be traced.
Warning: Thousands have bought the fake toothpaste, which may be contaminated with harmful chemicals, at Boots and Sainsbury's
In the past, fake Colgate toothpaste sold in the U.S. has been found to contain a toxic chemical used in anti-freeze.
That was made in China and it seems likely that the batch sold on UK high streets between November 28 and December 5 also originated in the Far East, although it was labelled Made in South Africa.
Customer Timothy Keen said he had been suspicious of the toothpaste because it had a peculiar smell and taste.
Mr Keen, 33, from Woking in Surrey, said: 'It tasted rather like Germolene, it was very odd.
'Looking on the internet, I found there have been health concerns about fake Colgate in the past. I am concerned about what has been put in the product, it could be anything.
'I can't believe a leading store can sell a fake product. Surely they should have checks in place.'
In a letter to the 17,000 customers who used their Nectar cards, Sainsbury's said: 'If you have any of this product at home, we would advise you to stop using it and return it for a refund.
'We are carrying out a full investigation and will take every necessary step to prevent a repeat.'
Warning notices have been put up in stores. In June last year, Colgate-labelled toothpaste sold in the U.S. was found to contain diethylene glycol (DEG) - a toxic chemical used in anti-freeze.
At the time, the U.S. Food and Drug Administration said DEG, sometimes used as a low-cost but potentially deadly substitute for glycerine sweetener in cough medicines, was a 'low health risk'.
Colgate in the UK said last night the fake product in Britain does not contain DEG, while Sainsbury's said it 'does not believe' the ingredients are harmful.
Colgate said there have been no reports of illness associated with the fake product, which was sold only in Boots and Sainsbury's.
Sainsbury's, which has notified trading standards authorities, added: 'We believed the supplier was reputable, and we are carrying out a full investigation.'
Boots said: 'We take the health and well-being of our customers extremely seriously.
'As soon as we were made aware of a possible issue with this product it was immediately withdrawn from sale.
'Customers that we know bought this product via our Advantage Card records have been contacted and we have issued a customer recall notice to be displayed in our stores.
'If any of our customers have any concerns, we would ask them to contact a member of our team in store or contact our Customer Care team on 0800 915 0004.'