The government is debating changes to the existing Forest Code The environmentalist had repeatedly warned of death threats against him by loggers and cattle ranchers.
The government has ordered an immediate investigation and promised to catch those responsible for their deaths.
The bodies of the couple were found inside the nature reserve, Praialta-Piranheira, where they had been working for the past 24 years.
According to family and friends, the pair had been subjected to numerous threats in the past two years for their environmental activism.
They made a living with eco-friendly cultivation of nuts, fruit and rubber.
News of the deaths came just hours before Brazil's chamber of deputies began debating changes to the existing Forest Code.
The legislation, first enacted in 1934 and subsequently amended in 1965, sets out how much of his land a farmer can deforest.
Regulations currently require that 80% of a landholding in the Amazon remain forest, 20% in other areas.
Proponents of change say the law impedes economic development and contend that Brazil must open more land for agriculture.
However, opponents fear that in their current form some of the proposed changes might give farmers a form of amnesty for deforested land.
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