The vaccine made by private Indian company Bharat Biotech has yet to be backed up with Phase III clinical trial results, the prosecutors at the Federal Audit Court, known as the TCU, argued in seeking an injunction.
The health ministry did not immediately respond to a request for comment.
Announcing the contract on Thursday, a ministry statement said the deal was worth 1.6 billion reais ($286 million), with the first 8 million doses expected to arrive in March.
The ministry published new rules last week dispensing with the bidding process to speed up the buying of vaccines and deal with the third biggest coronavirus outbreak in the world after the United States and India.
But the absence of late-stage trial results has raised criticism that right-wing President Jair Bolsonaro's government is cutting corners to make up for a slow roll-out of vaccines in Brazil, where more than a quarter of a million people have died of COVID-19.
The Bharat vaccine roll-out has run into trouble in India too.
The opposition-ruled state of Chhattisgarh in east-central India asked the federal government on Feb 11 to halt the supply of COVAXIN until its efficacy could be proven in an ongoing late-stage trial.
Bharat Biotech, which created the vaccine with the state-run Indian Council of Medical Research, has said efficacy data from the late-stage clinical trial of nearly 26,000 volunteers will be out by next month, leading to criticism from epidemiologists that it was approved too hastily for emergency use.