A decree issued by Bolsonaro authorises the deployment of soldiers in nature reserves, indigenous lands and border areas in the region, the BBC reported on Saturday.
The announcement comes after intense pressure from European leaders.
France and Ireland say they will not ratify a huge trade deal with South American nations unless Brazil does more to tackle blazes in the Amazon.
Finland's finance minister has also called on the EU to consider banning Brazilian beef imports.
Finland is currently president of the Council of the EU - a role which is rotated among member states every six months.
Environmental groups have called for protests in cities across Brazil on Friday to demand action to combat the fires.
Hundreds of protesters also gathered outside the Brazilian embassies around the world, including in London, Berlin, Mumbai and Paris.
"We can't stand around waiting for the sky to turn black all the way here in London too," protester Laura Villares House, 33, told BBC Brasil.
The largest rainforest in the world, the Amazon is a vital carbon store that slows down the pace of global warming.
It is known as the "lungs of the world" and is home to about three million species of plants and animals, and one million indigenous people.
UN Secretary-General Antonio Guterres tweeted on Thursday: "In the midst of the global climate crisis, we cannot afford more damage to a major source of oxygen and biodiversity. The Amazon must be protected."
Bolsonaro has said his government lacks the resources to fight the record number of fires in the region.
But conservationists have blamed his government for the Amazon's plight.
They say Bolsonaro has encouraged the clearing of land by loggers and farmers, thereby speeding up the deforestation of the rainforest.
The president has hit back at criticism, even suggesting that non-governmental organisations had started fires in the rainforest, despite admitting he had no evidence for this claim.
( With inputs from IANS )