The invasive gold clam discovered in the Waikato River in April had been there for two to three years, the Ministry for Primary Industries says.
Native to Asia and now found in North America, South America and Europe, gold clams have the potential to destroy native habitats, clog water supplies and hydro dams if not contained.
Efforts elsewhere to eradicate the pest have been unsuccessful as the clam is self fertile and are able to produce up to 70,000 juveniles a year.
Once established, densities can reach tens of thousands per square metre.
MPI officials gave an update on the response to the Waikato River incursion to the Primary Production and Environment select committees on Thursday.
Director of Readiness and Response John Walsh said the clam was well established.
"We think the clam has been in the Waikato River for at least two years - possibly two to three years.
"We can tell because of the density, the fact that it's in multiple locations and the size of the cockles, some shells are close to three centimetres and it takes about two to three years to grow to that size.
"It's well established, when we did our immediate delimiting surveillance downriver from Bob's landing the site where we initially found it, when we went up river we had no trouble finding it anywhere we looked."
Nationals spokesperson for biosecurity Nicola Grigg said the revelation is deeply concerning and efforts to contain the clam must be made immediately.
"It beggars belief it has only just been discovered - and by accident - meanwhile, MPI has spent the past month forming an industry advisory group rather than tackling the issue head-on.
"Full surveillance of the Waikato River and Lake Taupō is only just beginning, while tributaries won't be checked until the next phase of surveillance. Meanwhile, the threat of further contamination of waterways across the country is a very real possibility"
Grigg said without urgent action gold clams could infest Lake Taupō with the very real possibility it will make its way to hydro water schemes in the South Island as well.
But head of Biosecurity New Zealand, Stuart Anderson, stood by the response to date, telling the select committees the issue is being taken seriously.
"I'm ware there have been some concerns expressed around the timeframes and the activities that have been taking place taking place, to date since we became aware of this, we believe the actions we have taken have been appropriate."
Anderson broke down the history of the incursion which began on 19 of April when researchers doing some work around the Bobs Landing area spotted the clams.
The first notification of the finding was on 1 May, he said.
On 5 May there was visual confirmation that it appeared to be gold clam. "We had people on site doing inspections and some surveying along the river towards Hamilton.
"We then started the process of notifying councils, iwi and other key stakeholders."
On 15 May, the ministry received DNA confirmation that it was a freshwater gold clam.
After that there were hui with the river iwi, engagement with the councils and discussions on starting a surveillance programme.
"We got agreement on the methodology and the scope of the surveillance earlier this week, on Tuesday.
"That started on Wednesday and we're also getting work underway around doing some targeted inspection surveillance in other main waterways nationally that could be connected to the Waikato River."
Anderson said a technical advisory group of New Zealand and international expertise was being formed to give the best advice on how to deal with the clam.