The backpackers were travelling to Queensland's flood-hit North Burnett region from Brisbane but failed to arrive at their destination, police said.
The disappearance of the 26-year-old man and 23-year-old woman sparked a search of the Kilkivan to Mundubbera area, where floodwaters had recently inundated communities.
Police, SES volunteers and helicopters scoured the region from Wednesday morning, later locating a silver vehicle at Kilkivan Tansey Road.
Police late on Wednesday said the search for the tourists was ongoing.
It came as police issued an emergency declaration further southwest at Chinchilla on the Western Downs after floodwaters inundated another community.
An exclusion zone was set up in the town late on Wednesday, with authorities organising an evacuation area at the Chinchilla showgrounds.
At least 10 businesses were under water, sparking fears more homes would be lost to floodwaters.
The community northwest of Brisbane is next in line after Bundaberg was flooded on Wednesday, inundating hundreds of houses and businesses.
Chinchilla's flooded Charleys Creek is not expected to reach a 6.8-metre peak until about midday on Thursday, local mayor Andrew Smith told AAP.
Residents were clinging to hope that Charleys Creek, which runs through the town, would not reach the devastating flood levels of 2011.
Back then, Charleys Creek reached a record peak of 7.45m, flooding scores of homes and damaging the prized local watermelon industry.
"There are businesses that have been inundated at this point in time in those low-lying areas," Mr Smith said.
"But if it does get to that 6.8m peak, we will expect it to be more widespread in the town itself.
"Nature can be tough at times, and certainly nature gets its way. We can't do much about it."
But the significant rainfall has offered a silver lining for some locals.
"The sorghum harvest in most areas is probably finished, and it will be a bit of a godsend to those wanting to plant a winter crop," Mr Smith said.
Door-knocking began in the community's low-lying areas late on Wednesday warning residents to evacuate.
Flooding is also expected across the Condamine River and Myall Creek catchments.
Other peaks have been reported, with major flooding forecast along the lower Condamine River in the coming days.
As Chinchilla braces, Bundaberg to the north is reeling from its third major flood in 16 years.
The Burnett River peaked at 7.4m, short of the predicted 7.6m.
But flooding forced hundreds to evacuate, cutting power for about 2500 people.
The Northern Territory has also been hit hard by floodwaters, inundating remote communities and affecting the water supply.
Darwin and Palmerston residents were asked to conserve and boil water after flooding shut down a nearby dam's pumps.
Darwin locals have stocked up on bottled water, toilet paper and food, leaving some supermarkets' shelves bare.
Hundreds were airlifted from the remote communities of Daly River, Palumpa, Beswick and Jilkminggan at the weekend, mostly to Darwin.
The clean-up has begun at Katherine but hundreds remain in shelters.
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