The Ministry of Business, Innovation and Employment is probing problems with fuel on the Bluebridge Connemara ferry.
Contaminated fuel caused the ferry to lose power and drift more than two hours in the Cook Strait in September, StraitNZ confirmed on Friday.
The contaminated fuel damaged the ship's fuel injectors, which caused the power loss, chief executive Shane McMahon said.
The injectors were fixed and the contamination cleared, but the company was still looking into how and where the fuel was contaminated.
MBIE was also investigating, but the ministry itself had not confirmed the fuel was contaminated, its trading standards national manager Stephen O'Brien said.
"This matter is currently still under investigation and the existence or source of any potential contamination has not been confirmed at this stage," he said.
"This investigation will also include determining whether any potential contamination occurred on the vessel or in the supply chain."
It had tested samples of fuel supplied to the vessel and had not identified any problems with the fuel as it was supplied, O'Brien said.
"We have expanded our testing scope to include a number of historic fuel deliveries, and we expect these test results next week."
StraitNZ told the ministry on Monday that fuel may have been a factor in the Connemara's power loss, he said.
Resources Minister Shane Jones said he was not concerned about any widespread problems with fuel in New Zealand.
His office told RNZ he would await the outcome of MBIE's investigation.
Meanwhile, the union representing ship masters and officers said StraitNZ and Maritime NZ should have fronted up on the Connemara's problem immediately, in case it happened to any other vessel.
Maritime operators needed to know how to prevent further issues, Merchant Service Guild's vice president Iain MacLeod said.
But Maritime NZ said testing showed there were no problems with fuel supplied out of Wellington, and if there were, it would have notified appropriate people.
Transport Minister Simeon Brown said he was satisfied with Maritime NZ's communication to him and the public.
Sign up for Ngā Pitopito Kōrero, a daily newsletter curated by our editors and delivered straight to your inbox every weekday.