Eighty-five per cent of all births in Brazilian private hospitals are caesareans and in public hospitals the figure is 45%.
The new rules oblige doctors to inform women about the risks and ask them to sign a consent form before performing a caesarean.
Doctors will also have to justify why a caesarean was necessary.
They will have to fill in a complete record of how the labour and birth developed and explain their actions.
Each pregnant woman will now be assigned medical notes which record the history of her pregnancy, which she can take with her if she changes doctors.
The new rules are designed to reduce unnecessary surgical procedures, and ensure pregnant women are aware of the risks associated with caesareans.
However, experts say that a scarcity of maternity beds and wards equipped to deal with natural births means that for many women in Brazil, caesarean birth is seen as the best option.
"The best way to guarantee yourself a bed in a good hospital is to book a caesarean," Pedro Octavio de Britto Pereira, an obstetrician and professor at the Federal University of Rio de Janeiro, said in an interview with BBC Brasil last year.
Women who want to give birth naturally in a private hospital have reported finding all the beds are reserved for scheduled deliveries.
There have been numerous reports of women going into labour without a caesarean scheduled and being forced to travel from hospital to hospital in search of a bed.
Researchers say many women also see caesareans as more civilised and modern, and natural birth as primitive, ugly and inconvenient.
In Brazil's body-conscious culture, where there is little information given about childbirth, there is also huge concern that  natural birth can make women sexually unattractive.
Many doctors prefer caesareans too, as they can plan the time of a birth, and feel more protected from litigation.
Gynaecologist Renato Sa told BBC Brasil: "Doctors are responsible for what happens and in a situation of risk they chose a caesarean, because if there is a death or complication they will be asked why they didn't do this. Doctors are afraid of natural childbirth."

The governing body said it had been "deliberately misled" by the club about a deal to sell player transfer fee rights to an outside investor.
FC Twente says it will not appeal.
Fifa has banned third-party player ownership as a threat to the game's integrity because investors can inflate transfer fees to make a profit.
The Dutch FA says the punishment, including a 45,250 euros (£34,000) fine, follows Twente's failure to reveal full details of a third-party ownership contract with Malta-based Doyen Sports Investments.
The Enschede-based club won their only Dutch League title under Steve McClaren, now the Newcastle boss, in 2009-10 but are currently third from bottom in the Dutch Eredivisie.
FC Twente said that the sanctions would "hit hard at the heart of our club".
Twente's professional licence will be revoked if they fail to fully cooperate with an independent investigation into the club's structure, added the Dutch FA.
New rules have come into force in Brazil aimed at reducing the country's high number of caesarean births.
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FC Twente have been banned from European competition for three years by the Royal Netherlands Football Association.