Bolsonaro and his environment minister, Ricardo Salles, have taken issue with this interpretation of the numbers produced by a system known as DETER, saying they should not be used to measure month-by-month increases.
German diplomats could not be immediately reached for comment.
Brazil's far-right President Jair Bolsonaro on Sunday said his country does not need Germany's money after Berlin said it planned to cut $40 million in aid to preserve the dwindling Amazon rainforest.
In response, Bolsonaro said that his country doesn't need Germany's €35 million that had been earmarked for forest conservation and biodiversity.
Brazil is home to more than 60% of the Amazon rainforest, which is being cleared at an increasing rate to create more cropland.
An aerial view of a deforested plot of the Amazon at the Bom Futuro National Forest in Porto Velho, Rondonia State, Brazil, September 3, 2015.
The Amazon is vital to the exchange of oxygen for carbon dioxide in the atmosphere - a check on global warming.
Preliminary statistics from the space research agency INPE showed an 88 per cent jump in deforestation for June in the Amazon rainforest compared with the same month a year ago. But the Brazilian government has claimed the data is unreliable and misleading.
"Brazilian government policies in the Amazon raise doubts about continued, sustained declines in the rate of deforestation", German Environment Minister Svenja Schulze told the television news show Tagesspiegel.
Also on Monday, Pontes announced Darcton Policarpo Damião, a military officer, would be the interim administrator of INPE.
Among the projects that could suffer is the Amazon Fund, created in 2008 to receive donations to help prevent, monitor and combat deforestation in the Amazon. Germany is one of the fund's three main contributors.