(AFP) -- Russian President Vladimir Putin has ordered a crackdown on "destructive" non-government organisations, saying such groups were behind the mass protests that brought down Ukraine's government.

Moscow has repeatedly accused the new authorities in Kiev and the protesters who toppled pro-Moscow president Viktor Yanukovych of being extremists, nationalists and even "Nazis".

On Monday Putin told senior officials at Russia's FSB security service, the successor to the KGB, that "nationalist and neo-Nazi structures and fighters" in Ukraine had been financed from abroad through non-government organisations (NGOs).

"Russian legislation creates every condition for transparent free activities by NGOs, but we will never let them be used for destructive aims the way it happened in Ukraine," Putin said.

"We need to see a difference between civilised opposition to the authorities and serving others' national interests to the detriment of one's own country," Putin said in remarks released by the Kremlin.

Since returning to the Kremlin for a third term in 2012, Putin has tightened controls over NGOs, signing legislation forcing those with international funding to register themselves as "foreign agents."

In February, seven activists who took part in a rally against Putin's return to the Kremlin were jailed for up to four years and a prominent environmentalist who criticised the impact of the Sochi Olympics was jailed for three years over a protest.

Putin, who served as a KGB agent in East Germany, headed the service's post-Soviet successor, the FSB, between 1998 and 1999.