A judge is deliberating whether GNS Science should be tried alone, for alleged health and safety breaches at Whakaari / White Island.
On 9 December 2019, 47 people were on the crater when it erupted.
Twenty-two later died from extreme burns and blast injuries.
The Crown Research Institute is one of 12 parties facing a four month trial this year - alongside tourism companies and the island's owners.
On Thursday morning lawyers argued GNS was vulnerable to "collateral attacks" from other defendants on trial together.
Rachel Reed KC told the Whakatāne District Court: "There is a real prejudice to GNS. It's not a normal prejudice ... It's entirely collateral, and would bring GNS into the main trial in a much greater way than it should because the reality is it's not involved in allegations in relation to the eruption, but it will be drawn into the mix."
She argued that GNS' charge was different to all of the others, because it related to helicopter trips to monitor the island - but none on the day of the eruption.
"No one else faces the same charge, and they're [GNS are] not charged together with any defendant," she said.
"It [the charge] relates to the health and safety risks, arising from specific helicopter trips over the period of 2016 to 2019. And in fact, the last trip that GNS undertook was on the 4th of December, 2019, some five days prior to the eruption."
Reed estimated a separate trial done after the trial for all other accused, would take about eight days.
There were so far 48 "witnesses of fact" set down for the four months and only four would cross over into a split off GNS trial, she said.
Reed said separating the trials would allow witnesses, like helicopter operators, to give evidence in each trial, but Judge Evangelos Thomas challenged this.
"That is never how we would conduct a trial in respect of two parties [pilots and GNS] charged with failing to communicate properly with each other," he said.
Kristy McDonald KC, acting for WorkSafe, rejected Reed's arguments, and said some points "do a great disservice to the complexity of the evidence in relation to GNS and its importance to the main trial, the analysis again with respect to Ms Reed has been superficial and it's not right".
"There is an incredible commonality of allegation and an enormous overlap in evidence" between GNS and the other accused, she said.
In regards to the dates the charges related to, McDonald said: "It's the same risk, different day same risk. The charges against GNS, like the charges against the other defendant, allege a failure to adequately communicate risk."
Judge Evangelos Thomas will give a decision tomorrow.
RNZ
