The badges, which are awarded to viewers under 16 years old who contribute to the programme, are being displayed as genuine and are attracting bids of up to £104.
The BBC is looking at ways to verify that the badge belonged to its rightful owner and a spokesperson said that a large number of badges had already been taken off as a result of its intervention.
Richard Marson, Blue Peter's editor, said: "We know how hard children work to earn a badge and we are doing our best to ensure that this long-standing Blue Peter institution is no undermined."
The badges, which carry the programme's famous ship motif and are presented to competition winners, come in five types.
A gold badge is for outstanding achievements such as saving someone's life and they filter down to a blue badge, which is awarded for interesting letters, good ideas for the programme or appearing on the programme.
On Monday afternoon, there were 26 Blue Peter badge auctions, with prices ranging from 99p to £104.
An eBay spokesperson said: "EBay is committed to preventing fake items being sold on the site and we remove infringing items once an authorised representative of the rights owner reports them to us.
"However, there is no law preventing individuals who have been awarded genuine Blue Peter badges from selling them on eBay if they so wish."
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