Environmental groups have called the decision a “crime”.
Mangroves are an important protection against climate change.
President Bolsonaro’s policies and rhetoric on the environment have sparked widespread alarm, and the far-right leader has been accused of encouraging illegal activity.
The decision abolished the “permanent protection zones” created in 2002 to preserve Brazil’s many tropical mangroves and sand dune scrublands. It was taken by the National Environment Council, headed by the controversial Minister of the Environment Ricardo Salles.
Environmental groups say removing the regulations will allow real estate developers to clear large areas of natural habitats for tourism, which could lead to their destruction.
“These areas are already under great pressure from real estate development,” said Mario Mantovani, head of the environmental group SOS Mata Atlantica.
“The 2002 regulations at least protected them from further destruction,” he told AFP news agency, calling their repeal a “crime against society.”
One acre (4000 square meters) of mangrove forest absorbs almost the same amount of carbon dioxide as one acre of Amazon rainforest.
Since Mr Bolsonaro took power in January 2019, Brazil has been hit by environmental crises, including escalating deforestation and forest fires.
This is not the first time that the Minister of the Environment, Ricardo Salles, has been embroiled in a controversy since taking office.
In a leaked recording of an April cabinet meeting with the president, Mr Salles said the coronavirus pandemic was a chance to roll back environmental regulations “now that the media is only talking about Covid.”
“Even as we are witnessing record environmental devastation and Brazil ablaze, Salles is dedicating its time to promoting even more destruction,” environmental group Greenpeace said in a statement on the new measures.