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The Toronto-based company said independent director John McCoach would immediately replace Johnston on an interim basis.
Nautilus has had a turbulent 2018, the year starting with the resignation of previous chairman, Russell Debney, amid urgent talks to find US$10 million to keep development at Nautilus' majority-owned Solwara 1 copper-gold project off the coast of Papua New Guinea going.
Another $350 million is needed to get Solwara 1 to production.
Nautilus has had a hard time finding funding, although received a series of bridging loans from major shareholders this year.
On top of its financing woes, last month, a Chinese shipyard cancelled the contract for its more than half-finished production support vessel.
McCoach's mandate is to advance Nautilus' ongoing capital formation programme.
