The prime minister says $10 million in federal funds will ensure Brisbane's Cross River Rail project is properly integrated with other transport options.

Malcolm Turnbull announced the new money in Brisbane, saying the $5.4 billion project must be properly planned to get the best outcomes for Australia's fastest growing capital city.

Cross River Rail is set to receive its first installment of federal funding.

"The $10 million commitment we are making will enable that planning work and analysis to be done," he told ABC radio on Tuesday.

It's the first federal money set aside for the project.