The proposed restructuring, which would see a newly formed state agency gain control of the academy's 500 scientific institutes, "would lead ... to destruction and degradation of the country's scientific and defense potential and national safety," the academy's presidium said in an online statement.
The government has long accused the academy of being ineffective.
Russian-born Nobel Prize-winning physicist Andre Geim said while he agreed the academy was ineffective he was worried over uncertainty about the role and function of the state agency that would oversee many of the academy's functions.
"The uncertainty over this most important feature of the reorganization makes every Russian scientist anxious and worrying," Geim said in an email to RIA Novosti.
Draft legislation for the restructuring was submitted to Russia's lower house of Parliament last week, but a second reading has been postponed until fall.
In its statement the academy acknowledged reform was needed but criticized the government for not presenting the text of the bill to the academy or the general public before submitting it to Parliament.