The department store released the cuddly toy following the popularity of its festive advert - which features Paddington Bear converting a burglar into Father Christmas.
But M&S appear to have been caught short by a mad rush on the teddy after customers said the item had vanished from shelves and online - 45 days before Christmas.
Now eBay sellers keen for a quick buck have started flogging the bear online at more than twice its original price.
The bear is priced at £12.99 on M&S's online shop but is now being sold for up to £29.99 on the online auction site.
Sam Jackson wrote on the M&S Facebook page:
"I'm very disappointed M&S. I've been trying to buy a Paddington bear teddy all week.
"I've phoned all my stores plus looking on line and still can't find one. I'm dreading what my phone bill will be it's a shame so many have ended up on eBay at silly money!
"Please sort your stock out you must of known it was going to be popular!"
Lynda Finch-Jones, also posting on the page, said she had visited four stores in Wales without success and was told by a cashier in Swansea to "be quicker off the mark".
"She then said I've got mine, and proceeded to open a white cupboard behind the till, and took a bear out and showed it to us saying it was hers, that she had hidden it in there earlier and would be paying for it at the end of her shift!!!"
"Unfortunately I have not even been able to order a bear to be delivered to our local Llanelli store as they are out of stock..."
Replying to her post, M&S said they were "shocked" at the behaviour of the cashier and apologised.
"Not only is it wholly inappropriate to have made the comment about being quicker in future, the fact that she then got out the one she'd hidden away (AND not yet paid for) is just wrong.
"In terms of being able to get a Paddington for you, as you know they have been very popular, so any time more stock is added, they're pretty much gone by the following hour. We are due to get more in again, but we wouldn't expect this to be before next week."