Speaking to representatives from some of the world's leading rights and environmental organizations at the Civil G8 forum before Group of Eight leaders meet in St. Petersburg later this month, the president reiterated his main cause of anxiety.
"I personally - I will speak completely openly and honestly - have only one concern," Putin said. "I will always speak and fight against foreign governments financing political activity in our country, just as our government should not finance political activity in other countries."
Lawmakers and political scientists in Russia claimed while the bill was being drafted that NGOs had helped "color revolutions" in neighboring ex-Soviet countries, particularly Ukraine and Georgia, which swept away the ruling elite in favor of West-leaning authorities in 2004 and 2003.
The new law set more stringent and complicated financial reporting requirements for NGOs and has been criticized in the West and by liberal groups in Russia as being too restrictive and even as a step toward "authoritarian rule."
An espionage scandal in February, when British agents were accused of working in Russia under diplomatic guises and financing NGOs, did little to cool the atmosphere of debates. Putin said then he regretted that the incident, which involved a sophisticated communications device disguised as a rock, had cast a shadow on such organizations. But he said he would continue to support NGOs, though they would not be allowed to interfere in domestic affairs.
And today the president went a step further by admitting the law was flawed and promising that it would be reconsidered.
"I admit that this document has shortcomings," he said.
With over 700 people representatives of organizations such as the International Helsinki Group, Greenpeace, Amnesty International and Charities Aid Foundation attending the forum, the president urged NGOs to prepare comments about how the law was being enforced and pledged that they would be taken into consideration.
He also said he hoped the NGO law would not lead to tougher registration rules for foreigners.
"If it transpires that [requirements] are becoming more stringent [for foreigners], we will be prepared to react, and I am personally ready to initiate amendments, including those based on your recommendations," Putin told the forum.
The Federal Registration Service said that none of the 40 foreign NGOs that applied for registration after the introduction of the law had managed to complete the process. It said there were between 500 and 2,000 foreign NGOs operating in Russia, and that all of them had to re-register by October 18.
Sergei Tsyplenkov, the executive director of the Greenpeace office in Russia, said that new regulations were so unclear that they enabled officials to make harsh decisions at their own discretion.
But the registration service said the new registration procedure was transparent and "purely technical," requiring only that a number of forms be filled out, a task it said foreign NGOs had failed to do.
Russia is presiding over the club of rich nations this year and the leaders of the United States, the United Kingdom, Japan, Canada, France, Germany and Italy will be joining Putin in St. Petersburg for Russia's debut summit on July 15-17.