Biosecurity officer Hamish Lass said he was unsure how the crabs arrived but the discovery was devastating.
"We're not 100 per cent sure but it's most likely that larvae floated here or hitched a ride on a fouled hull or in ballast water from another part of the country. It's also possible they naturally migrated here as they are very capable swimmers."
Lass said Charybdis japonica was an extremely aggressive crab and an added threat to an already vulnerable ecosystem.
"These crabs are extremely invasive. Not only do they compete with our native crabs but they also feed on shellfish such as pipi, tuatua and cockles".
Lass said a response team led by the regional council and the University of Waikato was investigating the level of infestation in Tauranga Harbour and would also set up surveillance in the Maketu Estuary and Ohiwa Harbour.
The outcome could be grim, he said.
"Surveillance will help us determine the extent of incursion and what, if anything, we can do. If it shows they have established, they will be very difficult to contain as current control methods are limited in their effectiveness."
Tauranga mayor Greg Brownless said it was troubling news.
"Hopefully the response team are going to come up with great plan to figure out what they can do about it, and can quickly get on top of the situation, " he said.
"I hope there is not too much discussion and more action to eradicate this horrible pest from our harbour," Brownless said.
The regional council asks people to keep an eye out for Asian paddle crabs and said it was illegal to move living pest crabs.
The council encouraged people to kill them if they found any and report to 0800 STOP PESTS (0800 786 773).
What they look like:
Large swimming crab (up to 12cm across) with six distinct spikes on each side of the carapace and five spines on each claw.
Where they hide:
In New Zealand they prefer to hide in estuaries where there is firm sand or muddy fine sand up to depths of 15m.
Why they're a problem:
Extremely aggressive and have the potential to compete with native crabs for space and food. They also prey on native species such as shellfish, fish and other crustaceans. Rapid growth and reproduction rates mean they can establish themselves quickly.
