The exact location of a further 17 containers carrying the chemical was not known, after many went under with the Rena when it was ripped in half and sunk amid a January storm.
Among documents released to the party under the Official Information Act, the Environmental Protection Authority's principal scientist for hazardous substances, Peter Dawson, recommended monitoring for elevated levels of fluoride from the cryolite.
The contents of containers carrying ferrosilicon and one of potassium nitrate are also thought to have been lost at sea.
Another container of 5400kg of trichloroisocyanuric acid was on the seabed next to the wreck in March, but has not been recovered.
Professor Chris Battershill, who is overseeing a joint monitoring programme following the disaster, expected any effects on the ecology would be picked up in upcoming analysis of the sea floor around the wreck site.
The risk cryolite posed depended on the form of it, he told the Herald.
"If it's in block form, it's relatively inert and doesn't dissolve well, but if it's in powder form it can disperse, get into sediments, and we can have an issue," he said.
The substance was understood to be in mixed form, but that may have changed depending on the state of the containers holding it.
"We are concerned enough given the material is still there to have higher-focused surveys to look [at] exactly how it might have entered the environment."
Ongoing monitoring would also gauge the existence of tiny tar balls, some which were found on Papamoa Beach as recently as this month.
It was not known whether this oil was freshly released from the Rena, was old weathered oil that had resurfaced in the sand or driven ashore, or if it was from the ship at all.
A question mark also hung over whether oil had led to any sub-lethal effects on reproduction and repopulation of kaimoana species.
But the results of tests from the winter months - covering data from 30,000 samples - showed cause for optimism. Professor Battershill said there was still much work to be done.
Pollution:
Oil
Results from more than 30,000 samples have so far shown that levels of PAHs (Polycyclic Aromatic Hydrocarbons) have dissipated in most areas of the Bay of Plenty. But oil may have led to a reduction in some kaimoana species and there is still potential for lasting effects.
Hazardous substances
The contents of three containers of cryolite, a byproduct of the aluminium smelting process, have been lost at sea, while the location of a further 17 containers with cryolite is not known. Scientists will boost surveying.
Other chemicals
Maritime New Zealand sprayed about 200 litres of Corexit 9500, the controversial chemical used during the large spill in the Gulf of Mexico in 2010, to try to break down oil from the Rena in the early days of the disaster. Scientists have yet to test kaimoana species for traces of this controversial dispersant, but do not expect to find any.
