Young said port staff are happy they have recovered one of the shipping containers, but are still yet to locate the other.
A spokeswoman said the Port was supporting the efforts of the harbourmaster in a plan to secure and retrieve the container that had been found.
"Members of the public are advised to stay well clear of the empty container. We're yet to determine the location of the second container.
"A marine warning was issued to shipping and the boating community to notify of the hazard."
Hawke's Bay harbourmaster Martin Moore said it was certainly unusual for strong winds to throw shipping containers into the water.
"We've had them blow down before in bad weather, but we've never had them go into the tide.
"The containers that you see in the port are full and ready for export, they're not going anywhere, and they're usually 25-30 tonnes. These ones were empty so it's different story."
Moore thought it unlikely the other container would wash up alongside its companion.
"I'm guessing when it blew off the wharf it's landed on the rocks near the edge there.
The rocks would have probably punched a hole in it and it's now sitting on the seabed below the port."
Young agreed that it was the first time a container had ever ended up in the water because of the weather.
"At 45 knots, the wind gusts hitting Napier Port have been extreme and as far as we can recall, we have never had a container blown into the water like this before.
"Shipping is currently on hold until the weather clears but, once the weather allows it, we'll be using our pilot boat's sonar system to check the marine environment around the port to ensure the safety of shipping activities."
Moore said high tide was about 4pm yesterday which meant both the shipping container and buoy would sit safely on the beach until authorities shift them today.
Shipping activity also remained choppy because Hawke's Bay also experienced tremendous swells, with the largest recorded reaching 8.5m.
However conditions were easing as the subtropical front moved towards Taupo overnight before moving south.