WADA said in a statement it had been alerted by an accredited laboratory in Cologne that bottles manufactured by Swiss manufacturer Berlinger could be opened after being frozen.
The glass containers, known as the BEREG-KIT Geneva, were touted as the next generation of sample bottles after being released last year in the wake of the Russian doping scandal that dogged the 2014 Winter Olympics.
It was not clear if the new Berlinger bottles were due to be used at next month's Winter Olympics in Pyeongchang.
In its statement, WADA said it had "initiated an investigation into a potential integrity issue with the new generation BEREG-KIT Geneva security bottles and will recommend appropriate measures, if needed, in order to maintain the integrity of the doping control process."
The agency said it was alerted to the possible flaw by the Cologne laboratory on January 19.
The lab had found that the bottle "may potentially be susceptible to manual opening 'upon freezing' of a sample."
WADA said it had contacted Berlinger over the issue, and the Swiss company later responded that it had been unable to replicate the flaw found by the German laboratory.
"WADA acknowledges that this situation, if confirmed, will raise concerns and questions. We wish to reassure athletes and other stakeholders that WADA is resolutely committed to following up with Berlinger until the matter is resolved; and that, we will keep stakeholders apprised as the situation evolves," WADA added.
In the 2014 Sochi Olympics doping scandal detailed in a report by Canadian lawyer Richard McLaren, investigators discovered that Russian staff involved had developed a method being able to open "tamper-proof" sample bottles undetected.
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