The National Institute for Space Research (Inpe) said its satellite data showed an 83% increase on the same period in 2018.
It comes weeks after President Jair Bolsonaro sacked the head of the agency amid rows over its deforestation data.
Smoke from the fires caused a blackout in the city of Sao Paulo on Monday.
The largest rainforest in the world, the Amazon is a vital carbon store that slows down the pace of global warming.
Conservationists have blamed Mr Bolsonaro, saying he has encouraged loggers and farmers to clear the land.
Meanwhile, US space agency Nasa said that overall fire activity in the Amazon basin was slightly below average.
The agency said that while activity had increased in Amazonas and Rondonia, it had decreased in the states of Mato Grosso and Pará.
Why are there fires in the Amazon?
Wildfires often occur in the dry season in Brazil but they are also deliberately started in efforts to illegally deforest land for cattle ranching.
Inpe said it had detected more than 72,000 fires between January and August – the highest number since records began in 2013. It said it had observed more than 9,500 forest fires since Thursday, mostly in the Amazon region.