The health ministry stopped releasing cumulative totals for deaths and cases on Saturday, provoking uproar.
On Tuesday a Supreme Court judge ordered the government to release the figures amid accusations of censorship.
Brazil has the world's second-highest number of cases - and has now more daily deaths than any other nation.
Earlier, President Jair Bolsonaro said the change in policy was a result of actions being taken to improve Covid-19 reporting.
The health ministry said it would only report cases and deaths that had occurred in the past 24 hours.
But critics accused the far-right president's government of data manipulation, with Brazil's national council of state health secretaries describing the move as "authoritarian, insensitive, inhuman and unethical".
Supreme Court Justice Alexandre de Moraes told the ministry to "fully re-establish" the publication of Covid-19 data in the interests of public health.
Brazil has the world's second-highest number of cases, and has recently had more new deaths than any other nation.
The Latin American country has recorded more than 700,000 infections, but because of insufficient testing, the number is believed to be much higher. More than 37,000 people have died, the third-highest toll in the world.
Using data from alternative sources, Brazilian media outlets started publishing their own coronavirus figures to keep the public informed.
They criticised President Bolsonaro for his handling of the pandemic, during which he has opposed lockdown measures and downplayed the virus as "a little flu".
On Tuesday, the president reiterated his threat to withdraw Brazil from the World Health Organization (WHO), accusing it of not acting responsibly during the pandemic.
Last week, Mr Bolsonaro branded the health agency a "partisan political organisation", echoing comments made by US President Donald Trump, an ally of his.
The president has repeatedly joined supporters in protests in recent months, ignoring social-distancing advice.
What did the judge say?
In a statement on Tuesday, Mr Moraes said the health ministry must "fully re-establish the daily divulgation of epidemiological data on the Covid-19 pandemic", including on its website.
The judge made the ruling on Monday night in response to a legal challenge from three political parties.
Mr Moraes gave Mr Bolsonaro's government 48 hours to release the full figures again, O Global newspaper reported.
He said the health emergency in Brazil was so serious, it required all government agencies to "put into effect public health protection".
The judge "highlighted the disastrous consequences for the population if internationally recognised measures are not adopted, such as the collection, analysis, storage and dissemination of relevant epidemiological data".
What is the situation in Brazil?
Only the US has more coronavirus infections than Brazil, the most populous country in Latin America.
Health experts say infections are expected to rise even further, as the outbreak is still weeks away from its peak, putting more strain on hospitals.
Last month, Brazil's death toll surpassed that of Italy's, placing the nation third in the world, behind only the US and the UK.
Mr Bolsonaro has played down the risks of the virus, comparing it to "a bit of a cold". Two health ministers have left the post since the outbreak began in disagreement with the president's handling of the pandemic.
The president has continued to call for lockdown measures imposed by local authorities to be lifted, arguing that they will wreck the economy.
The president has also accused state governors and mayors of using the issue for political gain, as many who have taken stricter measures oppose his government. BBC