The police serious crash unit were investigating, and it was too early to tell whether alcohol or speed were factors.
Wellington Free Ambulance spokesman Chris Matthews said a 111 call, believed to have come from a local farmer, was received around 5.30am.
Emergency services found one youth inside the vehicle and another walking around.
The 16-year-old was freed from the car and taken to Wellington Hospital by the Westpac Rescue Helicopter in a critical condition.
The other was taken to Wairarapa Hospital in Masterton by ambulance, where he was treated for moderate injuries.
A fire service spokesman said Carterton volunteer fire brigade attended to assist ambulance and police but were not needed to cut the boys from the car.
Meanwhile nationally, the holiday road toll stood at one last night, after an elderly woman was killed in a crash near Hamilton yesterday afternoon.
Two people killed this week were not included in the holiday road toll.
A 3-year-old boy killed by a car in a driveway near Taupo was not included in the figures because the death did not occur on a public access-way.
Nor was the death of a man in his 40s killed in a collision in central Hawkes Bay on Monday morning because it happened a few hours before the official holiday period started.
The latest fatal crash occurred just after 12.30pm on Te Rapa Rd, Hamilton, killing a passenger.
The official holiday road toll period began at 4pm on Christmas Eve and ends at 6am on January 3.
Police have lowered their speed tolerance and are issuing tickets to drivers doing any more than 4km over the speed limit in an effort to keep the toll down.
