Cops swooped on the Nightjar bar in Hoxton, East London, where barmen were serving the Moby Dick drink.
It contained Laphroaig whisky, Drambuie, ale, bitters and a “whale skin infusion”.
The raid last week comes amid a Europe-wide ban on whale meat and products, except under strict restrictions in Greenland and Denmark.
The Metropolitan Police were tipped-off in October that the bar was serving whale skin illegally. The Met’s Wildlife Crime Unit and a UK Border Force officer raided the premises on December 3.
A police spokesman said: “One item from the premises was seized. This has been sent for analysis.”
No arrests have been made at the Nightjar, which describes itself on its website as “a hidden slice of old-school glamour”. Its drinks range from £9 to £17 a glass.
Bar bosses said it had been unaware the drink contained an illegal ingredient until the raid and has removed the drink from sale.
Nightjar director Edmund Weil said: “We did have a drink on this year’s menu which included a small amount of scotch whisky infused with a single 2 x 5cm strip of dried whale skin.
“The strip was purchased in a shop by an employee while on a trip to Japan in autumn 2011.
“Until the police visit, neither ourselves nor our employees were aware of the legislation under which the bottle was seized.
“In hindsight we realise that regardless of the legal framework around such products, it was an error of judgement on our part to include this on our menu, and we would like to offer our apologies to anyone who may have been offended by it.
“We have removed the drink entirely from our menu, which will be reprinted before Monday to reflect this.”
Native Greenlanders who use whales as subsistence food are the only Europeans allowed to kill or to eat them in strictly limited amounts.