HMCS Iroquois was tied up in Halifax about two weeks ago and will not sail until a complete assessment is done on the air defence vessel.
Cmdr. Jay Harwood says it's not clear how long that will take, but it leaves the fleet further diminished as more than a dozen of its vessels undergo regular maintenance, modernization and repairs.
Harwood says the rust problems were found in a machinery space on the vessel in mid-April during a routine inspection ordered after cracks were discovered on the 42-year-old ship in February.
He says the navy will have to decide whether to spend money to repair the aging command and control destroyer, which is due to be retired in a few years.
This latest problem has forced the navy to juggle some of its assets and pull Iroquois out of scheduled operations, including one last week in Norfolk, Va.