The center-right European People's Party, the biggest political faction in the European Union Parliament, has called for the E.U. bill, aimed at restoring damaged environments on 20% of Europe's land and sea by 2030, to be rejected.
The scientists' letter did not mention the EPP but responded to claims the group has publicly made about the law, including that it will reduce Europe's food production and threaten food security.
"Those claims not only lack scientific evidence, but even contradict it," the letter said.
The scientists said the biggest threats to food security were climate change and the degradation of nature - and action to restore nature and curb agricultural chemical use was needed to maintaining sustainable food production.
Food security is also driven by factors including food waste and access to affordable and nutritious food, the letter said.
The letter cited numerous scientific assessments including from the U.N.-backed Intergovernmental Science-Policy Platform on Biodiversity.
"Once policymakers are taking very confident steps into the world of misinformation and basically what we nowadays call fake news, then scientists have the authority to say 'stop'," said Guy Pe'er, who led the letter and is a scientist with Germany's Center for Integrative Biodiversity Research and the Helmholtz Center for Environmental Research.
In response to the letter, EPP lawmaker Christine Schneider said the group supported the E.U.'s green agenda, but had specific concerns about the impact of the nature law.
"There are studies and analyses which show very clearly that the Commission's proposal will lead to a decline in food production," Schneider said.
Asked to provide evidence to back up the EPP's claims, a spokesperson for the group shared studies including one published in the academic journal EuroChoices.
That study said reducing land and pesticide use would curb agricultural production, but it emphasized that looking at this trend alone failed to account for the impact of declining biodiversity on food production, or how preventing nature loss can boost farming output.
The nature bill is heading for two tight votes in the E.U. Parliament, the first on Thursday, and must also win approval from E.U. countries.
The 3,339 signatories are mostly environmental scientists, representing institutions including the universities of Athens, Bucharest, Delft, Helsinki, Oxford and Zurich.