Seven vehicles, including a bus with 18 passengers, were involved in the first collision which happened at 09:20 at Drumossie Brae near Inverness.
No-one was injured in this incident, police said.
A man in his 50s was airlifted to hospital following the second accident which happened at about 09:30 at the A9's Carrbridge junction.
The trunk road was fully reopened at about 11:30.
Police Scotland said the low-lying sun was a factor in the first accident, which also involved the drivers of a Ford Ranger, Ford Fiesta, Citroen C3, Volkswagen Passat, Mitsubishi Shogun and a Seat Ibiza.
The second accident involved the drivers of a a Volkswagen Crafter flatbed van and a lorry.
An injured man, who was in the van, was flown by air ambulance to Raigmore Hospital in Inverness.
Sgt Donnie MacKinnon, of Police Scotland's road policing unit, said: "We believe a contributory factor in the collision on the A9 at Drumossie has been the presence of a low lying sun, causing reduced visibility for drivers.
"It is fortunate no-one has sustained life-threatening injuries and that of course is the most important thing but these collisions resulted in two separate closures of the main A9 arterial route, which brought with it disruption for all road users.
"Whilst I would like to thank road users for their patience during the closures, it is also important to remind drivers of the importance of driving to the road conditions and adjusting their speed accordingly."
Two accidents, 10 minutes apart and involving a total of nine vehicles, shut stretches of the A9.