It came a day after he and his 36-year-old wife, Dawn O'Porter, attended the LDNY show and WIE Award gala sponsored by Maserati at Goldsmith Hall in London.
Gatwick Airport declined to comment specifically on O'Dowd's experience at the security checkpoint.
An airport spokesperson told MailOnline Travel: "All passengers are subject to the normal security screening processes at the airport.
"When young babies come through security we ask parents to carry them. If the scanning equipment picks up something, we have to check both the parent and the baby.
"We always try to handle these searches sensitively. 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. In some cases this will be over 100 millilitres."
MailOnline Travel has contacted O'Dowd's representative for comment.
After posting the tweet O'Dowd was flooded with messages of support from his 630,000 followers, including many parents who have had similar experiences while passing through airport security.
One Twitter user wrote: "At least they didn't make you drink his formula to prove it wasn't explosive. Heathrow did that to me."
Another user wrote: "Just plain dumb. My 10-year-old nephew got to keep his bottle of water, why can't a baby keep its bottle?"
O'Porter, a Guernsey-raised writer, clothing designer and television presenter who recently hosted the Channel 4 series This Old Thing, gave birth to the couple's first child, Art, in late January.
He achieved fame in the UK with roles in The Clinic and The IT Crowd, but shot to stardom in Hollywood thanks to his role as actress Kristen Wiig's love interest in the 2011 comedy Bridesmaids.
- Daily Mail
