The Russian president told cabinet ministers yesterday that the government should take into account the concerns expressed by the Council of Europe and Russia's own Public Chamber.
Accordingly, he said he was asking his chief of staff, Sergei Sobyanin, to draft amendments to the bill by the end of the week.
At the same time, however, Putin defended the bill as necessary to ensure the country's security.
"This bill is needed only to safeguard our political system against external interference and to protect our society and citizens from any terrorist or misanthropic ideology that could be spreading under this or that sign," Putin said.
Putin emphasized that the democratic process and the achievements of Russian civil society were the country's main asset. He said that in protecting itself against harmful influences, Russia should be careful not "to throw the baby out with the bath water."
The reaction from local nongovernmental organizations has been skeptical. Aleksandr Petrov, head of Human Rights Watch Russia, said he's seen it all before.
"This is a favorite tactic of the government: two steps forward, one step back," Petrov said. "This has happened several times with other bills, when the government tables completely Draconian bills and then Putin comes along and says it should be amended. That's what's happened again and again, and this is just one more episode."
The State Duma passed the bill on its first reading on 23 November by the overwhelming margin of 370 to 18 -- despite concerns raised by the United States and the European Union.
If passed in its current form, the new legislation would prevent international organizations from having representatives or branch offices in Russia. To operate in Russia, they would have to register as Russian NGOs and be financially independent of their head offices. It would also make them ineligible for most sources of foreign funding.
Among those threatened with closure by the bill are international human rights organizations, think tanks, foundations, and social-welfare and humanitarian-aid organizations.
Petrov of Human Rights Watch Russia sees the bill as an attempt to destroy the NGO community.
"That goes well in line with all recent developments in Russia," Petrov said. "After all, TV stations were taken under control by the state and the political opposition was largely marginalized. The last independent sector of Russian society remains the noncommercial and general public organizations, and it seems it doesn't go in line with Putin's perception of how the state should be controlled."
Oleg Panfilov of the Center for Journalism in Extreme Situations is another who believes Putin's invocation of the security threat is a smoke screen to hide other intentions.
"Any attempts by Putin or any other government official to say that extremist or terrorist organizations are operating under the guise of NGOs -- well, excuse me, but laws already exist for this," Panfilov said. "There's the Criminal Code and there's the Law on the Fight against Terrorism. If an NGO really does propagandize extremism or terrorism, then ways exist to pursue it by legal means."
Panfilov said it's not security but politics that really lie at the heart of the bill. Like Petrov of Human Rights Watch, he argued that Putin fears the independence of civil society:
"Most of all, the authorities are alarmed by what happened in Georgia and Ukraine, where it's clear nongovernmental organizations played a major role in the revolutions there," Panfilov said. "So the Russian authorities are trying, two years ahead of the parliamentary elections, to in some way clean up the nongovernmental space, in order to protect themselves."
Putin's claims to the contrary notwithstanding, Russia's human-rights organizations see the bill as the latest stage in a long campaign by the government to emasculate civil society.
They point out the elimination of most independent media, the subordination of regional elites to the center, and the weakness of parliament and the judiciary. Nongovernmental organizations, rights watchers say, are almost all that is left of the checks and balances to presidential power in Russia.
This week may show how the Russian president really regards what he himself describes as the "achievements of our civil society."