Weather conditions were clear and calm at the time, and investigations are continuing into the cause.
The company is closed today but anticipates reopening tomorrow.
NZONE Skydive General Manager Clark Scott said the company was fully supporting the two staff members involved, as well as family, friends and other staff.
"Our immediate concerns are obviously for the wellbeing of the staff involved, and we are not in a position to comment further on their injuries or speculate as to what may have happened."
St John spokesman Mark Tregoweth said the two patients had been transported by road to Queenstown with serious injuries.
From there they were taken to Dunedin Hospital by helicopter.
They are now in a stable condition.
Tregoweth said St John were called at 7.45am, were on scene by 8.10am and left to transport the patients to hospital by 9.05am.
NZONE Skydive business development manager Derek Melnick earlier said the pair were doing a tandem jump and wearing parachutes. One of the men was the most senior instructor at the company
He said they impacted the ground harder than normal in their usual landing place or drop zone.
Melnick said it's not clear what went wrong at this stage.
Photographer James Allan was at the scene.
He said both skydivers had severe leg injuries, and one had facial trauma and abdominal injuries.
He said landing "at that speed . . you're in for decent strife."
The police spokeswoman said they were called at 8.15am to an incident where the people "came to the ground not as planned".
Worksafe and Victim Support have been notified.
The NZONE statement said they are working closely with all relevant authorities including the Civil Aviation Authority, the Parachute Association and the wider industry.
This is not the first time skydivers have encountered misadventure in New Zealand.
Nine people died when their plane crashed at the end of the runway at Fox Glacier Airport in 2010.
Thirteen skydivers were forced to jump out of an aircraft over Lake Taupo in 2015 after suspected engine failure.
In 2013 a pilot escaped without injuries after his skydiving plane crashed into a line of trees around Parakai. He was carrying two skydivers who managed to jump before the crash landing.