Gibson said the exact circumstances were not clear, but the company was co-operating fully with the police to help them determine what happened.
"I am extremely upset that one of our pilot boats may have been involved in the death of a swimmer. I understand the pain this will have caused and I offer the family and friends of the swimmer my deepest sympathies for their tragic loss," he said.
"Ports of Auckland will be co-operating fully with the authorities as this investigation continues. Until the investigation concludes, I am not able to make any further comment."
Police last night told the Weekend Herald they were investigating the potential involvement of a boat, which had been identified, located and examined.
A police spokeswoman said the investigation was ongoing and no further information about what happened was likely to be released until Monday.
"The man's name is not expected to be released until relatives overseas have been advised. Police and Victim Support are supporting the man's family."
A man who was on a 360 Discovery Cruises passenger ferry said someone on the vessel spotted the body about "two miles" off the coast of Mairangi Bay around 4pm yesterday.
The witness said the man's right leg was missing up to his waist.
"It was a very distressing mental image."
However a police spokeswoman said police have ruled out a shark attack.
James Bailey, manager of 360 Discovery Cruises, confirmed one of the company's vessels was involved in the gruesome discovery.
"Our thoughts and condolences are with the family at this time," he said.
The witness said the dead man was wearing a wetsuit and it didn't appear he had been in the water very long.
The skipper stopped the boat and waited with the body until maritime police and the harbourmaster arrived.
The company that ran the ferry service had offered the passengers who had been on board counselling, the man said.
