The cigarettes, which are branded “Palace” and are thought to be counterfeit, were found concealed inside a container which had been shipped from Singapore via Zeebrugge.
Staff said the cigarettes would have cost the Treasury about £2.5m in lost duty had the consignment got through.
Border Force spokesman Sam Bullimore added: “This is a significant haul, which would have defrauded the public purse out of a large amount of money.
“This is the latest in a series of large cigarette and Class A drug seizures we have made at our Humberside ports. Make no mistake – we are determined to make life as difficult as possible for those involved in this kind of illegal activity.
“We would encourage anyone with information about suspected smuggling to get in touch.”
The seizure, which was made on Monday, November 5, at about 2pm, follows other recent successes at the port against major smuggling operations.
In September, more than £6.5m of cocaine hidden on coal ships by Colombian drug cartels was uncovered, smashing one of the largest smuggling routes into the region ever known.
The high-purity cocaine was found hidden in loads of coal on bulk vessels that had travelled from Puerto Prodeco in Colombia.
About £5m worth of cocaine was discovered on a cargo ship at the port on August 13, and in June 20 kilos of the drug, with a street value of about £1m, were seized by Border Force officers.
Both ships had also sailed from Colombia.