The remarks by FSB director Nikolai Patrushev came as another government agency said nearly two-thirds of the country's NGOs had disappeared since 2002.
"Emissaries of foreign terror and religious extremist organizations, exploiting socio-economic problems and ethnic and religious differences, are trying to conduct recruiting efforts," Patrushev told law enforcement officials in televised comments.
"Individual foreign nongovernmental organizations provide information support to them to a large extent," he said.
He did not appear to identify any particular organization.
"An analysis of the situation in [southern Russia] provides evidence that bandits and their accomplices are engaged in an ideological fight for young people to replenish their ranks," Patrushev said, Interfax reported.
The Federal Registration Service, meanwhile, said the number of NGOs operating in Russia had dropped from 600,000 in 2002 to 227,577 in 2007, Vedomosti reported Tuesday.
The drop in figures led some aid workers to speculate that the trend would get worse before it gets better.
"We are already forecasting that a mass liquidation of NGOs will occur this summer," Maria Konevskaya, director of the Resursny human rights organization in St. Petersburg, told Vedomosti.
Konevskaya predicted an additional 15,000 to 20,000 NGOs would close this year.
President Vladimir Putin and his successor, Dmitry Medvedev, and others have criticized the work of nongovernmental organizations such as human rights groups.
Putin has defended new tighter regulations on NGOs as a way to make sure they are not controlled by what he calls puppeteers from abroad.
In 2007, the first full year the new regulations were in effect, more than 11,000 NGOs were denied registration and 8,274 registered groups were closed by court order.
MT, AP
A Message from The Moscow Times:
Dear readers,
We are facing unprecedented challenges. Russia's Prosecutor General's Office has designated The Moscow Times as an "undesirable" organization, criminalizing our work and putting our staff at risk of prosecution. This follows our earlier unjust labeling as a "foreign agent."
These actions are direct attempts to silence independent journalism in Russia. The authorities claim our work "discredits the decisions of the Russian leadership." We see things differently: we strive to provide accurate, unbiased reporting on Russia.
We, the journalists of The Moscow Times, refuse to be silenced. But to continue our work, we need your help.
Your support, no matter how small, makes a world of difference. If you can, please support us monthly starting from just $2. It's quick to set up, and every contribution makes a significant impact.
By supporting The Moscow Times, you're defending open, independent journalism in the face of repression. Thank you for standing with us.
Remind me later.