Ministry spokesman Mikhail Kamynin said the bill "takes into account" recommendations by Russian and foreign NGOs, as well as representatives of foreign states.
The bill yesterday passed its third reading in Russia's lower house of parliament, the State Duma.
It goes next week to the upper house Federation Council, where it is expected to pass easily before moving on for signing by Russian President Vladimir Putin.
Critics of the bill fear it will put a stranglehold on the work of NGOs, which represent one of the last independent sectors in Russian society.
But the government said the measures are needed to prevent NGOs from laundering money or promoting foreign political agendas.