Foreign spies are using charities and other groups in Russia as a cover for their activities, Moscow's foreign intelligence service chief says.
Condoleezza Rice condemned the draft changes
Non-governmental organisations (NGOs) and charity groups were very attractive for foreign agents, Sergei Lebedev told a pro-Kremlin newspaper.
He said tighter regulation of NGOs was necessary for state security.
Mr Lebedev's comments come as Russia's parliament debates legislation which would increase controls over NGOs.
There has been a storm of international protests over the proposed law, with US Secretary of State Condoleezza Rice expressing concern over the situation during a visit to Ukraine on Wednesday.
The proposals have been strongly criticised by both foreign and domestic non-governmental organisations.
Groups including Amnesty International and Human Rights Watch have said if it passes in its current form they may have to close their Russian offices.
When Mr Lebedev was asked in the interview with Rossiskaya Gazeta if he thought foreign secret agents worked in NGOs he said: "Yes, we have such information.
"Humanitarian missions and non-governmental organisations are very attractive for all secret services in the world. Secret services need cover, a mask, a screen," he added
The BBC's Emma Simpson in Moscow says Mr Lebedev's comments are similar to those made by President Vladimir Putin earlier this year, when he made it clear that Russia would not tolerate politically active NGOs that received money from abroad.
Russian officials believe that such money was used to foment the popular unrest that brought a change of government in Ukraine and Georgia, and they do not want it to happen in Russia, our correspondent adds.
On Wednesday, Ms Rice voiced concern about the draft legislation, which would restrict NGOs activities and require them to register.
She said the US government had spoken about the bill to Russia "at all levels".
Ms Rice said she hoped Russia would understand the role of NGOs in ensuring a "stable democratic environment".
The bill has passed a first reading in the Russian parliament, but our correspondent says it now seems likely that some of the details will be changed before its crucial second reading later this month.
But judging by the comments from the senior Russian intelligence official, the thrust of the new bill will remain unchanged, she adds.