It was hoped the ship would be back in action by the end of the week.
Sailings are still continuing on the Kaitaki and Kaiarahi.
The latest setback comes as the Aratere sports a flash makeover after it was refurbished in Singapore over winter.
The ferry has previously cost taxpayers between $25 million and $30 million in repairs, lost revenue and stand-in ferry costs after it lost a propeller.
Mathews said the current rudder investigation had nothing to do with the propeller which caused issues with the ship in 2013.
Ferry services were disrupted last week after towering 10m swells in the Cook Strait made it too dangerous to sail.
Timeline
• November 5, 2013 - Aratere loses a starboard propeller.
• December 2013 - Aratere is cleared to sail as freight only.
• January 2014 - Aratere is berthed in Wellington, and the Stena Alegra enters regular service.
• March / April 2014 - Aratere is dry-docked in Singapore for the first time.
• April 2014 - Aratere is berthed, awaiting new rudder stocks, maintenance continues.
• May 2014 - Aratere's second dry-dock to replace rudder stocks.
• June 2014 - Aratere departs after undergoing shaft alignment, sea trials and repairs and the Stena Alegra finishes services.
• July 2, 2014 - The Aratere due to arrive back in Wellington.
• September 13, 2016 - The Aratere has sailings cancelled due to mechanical problems