Ferguson Marine has been warned it may be forced to stop trading, after missing a deadline to file accounts.
The Port Glasgow shipyard is building two CalMac ferries, although their cost is now more than double the original contract price, with delivery more than five years late.
Companies House has issued a public notice that it could strike off the business if it fails to file the accounts, which were due at the end of December.
The accounts require the approval of MSPs before being submitted to Companies House.
Ferguson stated that it expects the accounts to be submitted by the end of March.
Chief executive David Tydeman told the BBC that auditors Grant Thornton were handling "outstanding issues" with the Scottish Government and Audit Scotland.
He said the reasons for the delay were "beyond the directors' control".
It is expected that Ferguson will have to pledge to cover its losses over the ferries before auditors sign off the company as a going concern.
Tydeman said: "We have been assured that Ferguson Marine will not be removed from the register provided we meet the undertakings we have given on filing by the end of March.
"The directors and management team remain fully committed to delivering the two hulls currently under construction and winning new contracts to secure the yard's future.
"This short term issue does not affect our ability to keep trading and continue the work in progress."
The shipyard fell into administration and was nationalised in 2019 amid a dispute between former owner Jim McColl and the government's ferries agency Caledonian Maritime Assets, which both blamed each other for the problems.
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