The ground investigations will begin on 26 September and are expected to be completed by the end of November.
The investigations will affect the Tay Crossing to Ballinluig, and Pitlochry to Killiecrankie sections.
The work is being carried out as part of the A9 dualling programme.
The traffic management arrangements will include short, alternate single file sections controlled by temporary traffic lights.
A Transport Scotland spokeswoman said the traffic management measures will allow work beside the carriageway to be carried out safely.
She said: "This ground investigation is needed to get vital information on the existing ground conditions in the vicinity of the A9 carriageway between Tay Crossing and Ballinluig, and Pitlochry to Killiecrankie as we progress our plans to dual this section of the route.
"This is the latest in a series of ground investigations taking place along the route.
"No decision has been taken on the line of the route for the section between Dowally and Ballinluig at this time and so that section is not part of the contract that has been awarded.
"We apologise for any inconvenience these works will cause and would thank road users and local communities in advance for their patience over the next few months.
"The contractor will closely monitor the operation of the traffic management measures to ensure that delays are kept to a minimum."
Traffic restrictions will be placed on two sections of the A9 for over two months for surrounding ground to be surveyed, Transport Scotland has confirmed.