The EIS was prepared by an external consultancy, Coffey Natural Systems, and helped Nautilus secure a 20-year mining lease last year.
Last week an independent review commissioned by the Deep Sea Mining Campaign, which has an association with the environmental lobby group Friends of the Earth, and conducted by Austides Consulting, raised concerns about the EIS.
Austides Consulting's general manager, Dr John Luick, told ABC Radio Australia's Pacific Beat program that the statement did not include data on ocean currents, which could carry mining waste into PNG's coastal waters and potentially affect fishing and other activities.
However, Nautilus' Chief Executive Mike Johnson, denied this.
"Their allegations are somewhat flawed," he said.
"The current data and all the environmental data that was collected and submitted to the government was reviewed externally."
The EIS was subjected to a peer review by the Australian-based consultancy, Cardno, but the PNG government has yet to make the results of that review public.
Dr Brian King, the oceanographer who used ocean current data to simulate the effect of the mining process for the EIS, said he is confident his assessment is correct.
"I can confirm that the ocean current data was used in those calculations," Dr King said.
"We found that those currents were weak, and they're significantly tidal . . . and because the currents are so weak, it was not surprising that any discharges that take place at that depth are likely to remain localised."
Meanwhile, Mr Johnson said he wants to resolve a financing dispute with the Papua New Guinea government that prompted it to suspend work at a site near New Ireland Province.
Building work at the site stopped on Tuesday night, with Nautilus saying it was owed more than $US70 million in development funding and capital contributions by the PNG government.
Mr Johnson said he is hopeful of reaching a deal that would satisfy both sides, but said no timeframe had been set.