The Spirit of Britain will be unable to sail until the issues have been addressed, and surveyors said they "did not know" when this would happen.
It comes after the line’s Pride of Kent vessel was detained last month after it reportedly failed a safety inspection.
In a statement to the BBC, the MCA said: "We have advised P&O [Ferries] to invite us back once they have addressed the issues. We do not know yet when this will be."
P&O Ferries’ Dover-Calais routes are currently suspended and the company has said it will not resume services on the route before Friday (15 April).
It comes after the firm sparked outrage by replacing all 800 crew with agency workers paid less than the minimum wage.
