Nautilus had agreed to pay Marine Assets Corporation (MAC) $10 million of an $18 million charterer's guarantee for a vessel to be deployed for use at the company's Solwara 1 copper-gold project off the coast of Papua New Guinea.
The money was to be paid in November once a shipbuilding contract became effective, but in December, Nautilus discovered the funds had been paid into a bank account it believed to be MAC's but was not.
Nautilus said it and MAC had been the victim of a cyber-attack by an unknown third party and the matter was referred to police, who are conducting an investigation.
A cyber security firm has also been engaged to investigate and ensure the ongoing security of the two companies' networks.
Nautilus has agreed to prepay $10 million to MAC on the basis that the remaining $8 million will be provided once the vessel is chartered and when the parties have agreed to determine how to proceed in relation to the deposit on completion of the investigation.
The company warned it could take some months to complete the investigation.
Last week Nautilus announced its collecting machine - the second of three seafloor production tools - had been assembled and was being commissioned.
"This is an exciting time for the company as we continue with the build of the seafloor production equipment while work has also started toward the build of our production support vessel," Nautilus CEO Mike Johnston said.
Toronto-listed Nautilus is aiming to begin seafloor mining by early 2018.