The Deep Sea Mining Campaign and Greenpeace have claimed a speculative rush to mine the seabed, with companies in an unholy alliance with the agency responsible for regulating it.
The NGOs want a moratorium on seabed mining, and exploration, for 20 years, until more is learned about its impacts.
In a letter, the secretary-general of the ISA, Michael Lodge, did not respond to the NGOs' claims that he is too close to the mining companies or the call for the moratorium.
But he said the industry is subject to one of the most complex and ambitious systems of global governance that humanity has yet devised and is still working to determine how this might be implemented.
Mr Lodge said no activity will be allowed if an environmental impact assessment indicates an undue impact.
But the Deep Sea Mining Campaign's Helen Rosenbaum said the only assessment that had been done is an impact statement from mining company, Nautilus, that was flawed and not fit for purpose.