The man, who is believed to be 61, has been taken to a local police station and has been bailed until next month.
The incident is being investigated by Heathrow CID and has not been passed to Scotland Yard's counter terrorism branch.
A spokesman for Cathay Pacific, a Hong Kong based airline, said: "Cathay Pacific can confirm that CX254 was delayed due to a crew-related incident concerning some items found in the pilot's hand luggage.
"At no point were passengers or staff put at risk. Given timings, Cathay Pacific were unable to organise a relief crew and therefore passengers experienced an overnight delay. Cathay Pacific takes this very seriously and is liaising with the relevant authorities.
"The airline assisted passengers with overnight accommodation and alternative flight arrangements."
They added that the Boeing 777 flight had departed at 14:47 BST on Sunday and arrived in Hong Kong at 09:31 BST on Monday.
- Independent