Two Cook Strait ferry captains have been stood down amid allegations of three serious incidents on the Interislander crossing, KiwiRail has confirmed.
However, the suspension of two skippers would not have a major impact on ferry timetables, the company said.
It follows allegations by New Zealand First leader Winston Peters yesterday that KiwiRail was attempting to "cover up" the three incidents, which took place in the last five days.
Two Interislander ferries, the Arahura and Kaitaki, were involved in a near miss at Picton early last week, Mr Peters alleged.
In an incident on Sunday, when the Arahura was leaving Wellington, the pilot on the nearby cruise ship Dawn Princess told the Arahura skipper to take a certain bearing but the skipper turned in the opposite direction and nearly hit a third ship, the Citrus Express.
The third incident involved the Stena Alegra, which has a damaged propeller, Mr Peters said.
"Reliable sources have told us this happened when the ship hit a wharf in Picton."
Today, the company confirmed two of its ferry masters were stood down while investigations took place but denied it would impact on business.
"While we may need to move masters between ships, this is a quiet time of year and there should be minimal impact on freight and passengers," a spokeswoman said.
Interislander general manager Thomas Davis yesterday rejected claims of a cover-up over the three incidents.
"No cover-up has occurred, and in the case of one of Mr Peters' claims that recent damage to the Stena Alegra propeller occurred because the ferry hit a wharf in Picton is quite simply, wrong."
Safety was Interislander's top priority, and the organisation encouraged a culture of full incident reporting as a matter of practice to maintain its high safety record, Mr Davis said.
Mr Peters' two other claims of a cover-up also could not be supported, he said.
Mr Davis also stressed that reporting in itself didn't necessarily mean a safety incident had occurred.
"The incidents Mr Peters alleges have been subject to normal investigation protocols and a full safety investigation has begun, including the opportunity for all parties to share incident details to establish if further action is required.
"Our internal investigation team is examining these alleged incidents, including taking steps to ensure our staff are treated appropriately through the investigation process," Mr Davis said.
Maritime New Zealand said it was investigating all of the incidents.
Mr Davis said KiwiRail reported to Maritime New Zealand as a matter of course.
"As with every investigation, staff allegedly involved were stood down and as part of our standard procedures undertook drug and alcohol testing."
Transport Minister Gerry Brownlee has also been briefed on the incidents.
Reported near miss incidents between January 2011 to December 2013 involving all Cook Strait shipping operators:
* Maritime New Zealand received 68 incident reports of all types in that period for all ferry companies operating in Cook Strait;
* of these, 15 were reported as near miss, or close quarters incidents, for all ferry companies;
* Interislander was involved in 36 reported incidents, and 10 near misses; and
* Interislander conducted 60 per cent of all ferry crossings and has less than 50 per cent of reported incidents.