Anthony Albanese said he would consider proposals to save the company, but added Rex already received substantial public funding with "no conditions attached".
"One of the things I expressed concern about was having no conditions, so Rex, for example, moved away from their traditional role of being a regional airline and into flights, for example, from Sydney to Melbourne," Albanese told reporters.
Rex began servicing Sydney-to-Melbourne, one of the busiest routes in the world, in 2021.
As of Tuesday afternoon, Rex's website showed no available flights from Wednesday onwards.
"Now Rex, as a regional airline, of course, provides important links with regional communities, and particularly between capital and regional communities is important for those local economies," Albanese said.
"We want to see the aviation industry in Australia continue to be one that provides services and access."
Regional Express' shares went into a trading halt on the Australian stock exchange following recent boardroom turbulence and multimillion-dollar earnings losses.
An announcement is expected by the opening of trade on Wednesday.