The actor, 35, was travelling through Gatwick airport with his three-month-old son when the incident occurred.
Taking to Twitter to share his ordeal, the Bridesmaids star revealed the security staff also took away Art's bottle.
Chris wrote: "Thanks Gatwick security! Some might think body-searching a baby and binning his bottle was over zealous and weird, but not me! #scarybaby"
However Gatwick defended their policies, insisting all passengers are treated the same.
A spokesperson for the London airport told the MailOnline: "All passengers are subjected to the normal security screening process at the airport.
"When young babies come through security we ask parents to carry them. If they scanning equipment picks up something, we have to check both the parent and the baby."
They also addressed Chris' complaint about Art's bottle, adding: "The restrictions around liquids are government requirements, and passengers are advised that when travelling with a baby they are allowed to take enough baby food, baby milk and sterilised water for the journey."
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