The 33-year-old has been charged days after his 27-year-old partner was found dead with "visible facial injuries" in a Jeep Cherokee near the Northern Territory's Tennant Creek.
The pair had been on a cross-country trip from Queensland when the man rang emergency services about 5.50am on Sunday, police said.
He allegedly said the woman was not breathing after their car hit a kangaroo on the highway near Barkly Homestead.
The woman was found dead at the scene with facial injuries, NT Police Acting Commander Mark Grieve said.
The man also had "some injuries".
Further information obtained at the time led officers at the scene to believe the woman had been assaulted by the man earlier that morning, he said.
The couple had been in the Jeep parked on the side of the Barkly Highway from 1.30am to 5.30am, police had earlier alleged.
Her death was treated as suspicious and the man has been in custody at Tennant Creek since.
Police released a photo of the Jeep which showed damage to the front of the vehicle.
Mr Grieve told reporters on Thursday investigators were trying to determine whether the damage was "pre-existing or whether it was fresh".
"At this point in time, we haven't been able to locate any evidence of that particular (kangaroo) strike occurring," he said.
An autopsy was under way to determine a cause of death, he said.
The couple's movements leading up to the death have been traced by NT Police working closely with their Queensland counterparts.
They are believed to have been on a trip since April 1, driving from Gympie in Queensland through to the NT's Barkly Homestead over four days.
The man was charged with murder on Thursday night, NT Police confirmed.
He is expected to appear in Alice Springs Local Court on Friday.
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