The federal body charged with assessing the merits of Brisbane's proposed $5.2 billion Cross River Rail has contradicted claims it had no concerns.
Queensland Deputy Premier Jackie Trad on Friday claimed Infrastructure Australia had no issue with the business case, after Prime Minister Malcolm Turnbull questioned the project.
"Yesterday afternoon senior officials from my agency and the Director-General of the Premier's Department phoned Infrastructure Australia and asked if there was any outstanding items," Ms Trad told ABC Radio on Friday.
"What the officials are saying is very different from what the politicians are saying on this."
But Infrastructure Australia on Friday said it did have concerns about the proposed rail tunnel.
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"IA has a number of outstanding concerns with the Cross River Rail business case and we have advised the Queensland government of these concerns," a spokeman said in a statement.
"We are working with the Queensland government to address these and we hope to be able to finalise our evaluation when they are addressed."
Mr Turnbull identified three issues with the project's business case during a meeting with Premier Annastacia Palaszczuk on Thursday.
More work was needed on integration, land use opportunities and general development, he said.
Ms Trad said it was unfair for the federal government to fund big projects in Sydney and Perth and then ask asking Queensland to pay for a second Brisbane River crossing.
"This is a farce, there is inconsistent rules for different infrastructure projects across the country," she said.
"The prime minister should be a prime minister for the whole of Australia."
Federal Treasurer Scott Morrison denied this.
"We're getting a lot done in New South Wales because they just want to work with us and we welcome that approach and we would welcome that here in Queensland," he told reporters in Brisbane.
The federal government has funded a $530 million upgrade of the Bruce Highway between Pine River and Caloundra north of Brisbane and a $120 million to remove a significant bottleneck at Deception Bay.
"These are our priorities and this is where we're putting our money," Mr Morrison said.
The state government may have to find money for the river project in its own budget to be handed down on June 13, or delay it further.
