The project, which is not due for completion until late next year, will begin on Tuesday.
The $200 million initiative, to affect RAAF Base Darwin as well as Darwin International Airport, will help support military and civilian air traffic into the Northern Territory until at least 2040.
The first phase, expected to be completed in early October, will reduce runway length but will not impact operations.
The second will follow immediately and run until the end of November.
Phase two will involve the closure of the main runway daily from 2am to 11.30am, with regional airline traffic directed to operate from a secondary runway if required
Work will come to a halt at the start of the Top End's wet season and recommence in April next year with an updated schedule for 2024 to be released in October.
Some disruption was unavoidable, according to the Department of Defence.
The secondary cross runway at the airport does not have lighting to support night flights and is neither long enough nor strong enough to support large airliners.
Major traffic could not, therefore, be diverted.
As well as being a public facility, the runway at RAAF Base Darwin is considered a vital military asset and has supported peacekeeping efforts, casualty evacuations after the 2002 Bali bombings and relief efforts in Indonesia after the 2004 tsunami.
The base also received Australians repatriated due to COVID-19 and assisted with the reception of evacuees from Afghanistan in 2021.
Airport Development Group chief executive Tony Edmondstone said airlines could review impacts and provide certainty to the travelling public now the works schedule had been finalised.
"Air connectivity is crucial for Territorians and these works are essential to support the safe and efficient operation of the airport for the next couple of decades," he said.
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