He believes the crafty toy wound its way through the kitchen, lounge, up a flight of stairs and across a bedroom before leaving through the bedroom door.
The sharks can be left on a neutral buoyancy weight by placing plasticine on their noses, leaving them floating in the air before using a remote control to move them up, down or sideways.
Once lost, he promptly set about asking around for the missing toy with a "nice smile and sad eyes."
"It was Christmas morning and I was going around asking the neighbours, had they seen a shark swim by, and they get weird looks on their faces."
Mr Thompson also posted a 'missing shark' listing on Trade Me, since which he has had more than 600 emails "ribbing" him or telling of fellow shark losses and sightings.
"For the $80, I suppose we've had a lot of laughs and a lot of humour about it, but it really brassed me off to lose it."
Another Hamilton resident, who lives on the outskirts of the city, contacted Mr Thompson to share his own story of a lost shark.
The man had blown up the shark in his garage and said the inflated toy made its way out through five rooms before heading out to the wide unknown.
Mr Thompson now believed his own helium-filled toy could have migrated down to Christchurch, where a flying shark toy was sighted by a pilot one day later at 2000 feet.
"I understand it's been seen over Christchurch. It was lost at about the same time. They're cunning characters, these sharks."
Civil Aviation Authority spokeswoman Emma Peel said she had received one report of a floating shark toy on Boxing Day.
"According to the report we received, an aircraft on approach into Christchurch at 2000 feet got an estimated 100m from it."
She the plane was 5.5 nautical miles south of Christchurch, and did not get close enough to the shark to change the flight path.
She said the sighting would not be investigated as it was not of particular worry to pilots.
Although this was the first incident involving an inflatable toy, Ms Peel said the authority has dealt with a number of incidents in the past involved inflated items.
"We've had examples in big cities where maybe car dealers build quite large things, floating off their sites, and we have had instances of those breaking free. And often you see a mass helium balloon release, and pilots have reported sighting flocks of those going past."
Ms Peel warned any owners seeking lost sharks to contact police.
Multiple sharks have been reported missing in the New Zealand Herald column Sideswipe, one of which was last seen flying over Pukekohe, heading for the west coast.
The column also reported a sighting by a pilot on the Wings Over New Zealand Aviation Forum, where a shark was spotted about 1500 feet above Hamilton city several days after Christmas.
