Putin told civic leaders attending the Civil Summit of the G20 group of major economies in Moscow that he had heard complaints about the new law.
"I agree with our colleagues ... About the need to analyse the practise of how (the law) is applied," Putin said in televised remarks.
"We should think about improving this legislation so that it does not bother anyone," he said.
The measure slaps NGOs enjoying Western funding and practising activities seen as political with a "foreign agent" tag that in Russian implies that the group is working as a spy.
Those that refuse to register under the new law but are deemed to be Western money recipients are subject to stiff fines and potentially limited in their future work.
The law was passed after Putin accused the West of funding street protests that rose against his rule in the runup to his March 2012 presidential election to a third term.
Officials said that hundreds of Russian groups may be branded as foreign agents as a result.
Many -- including London-based Amnesty International and the New York-based Human Rights Watch -- have already had their offices searched by prosecutors.
The authorities have also hiked fines on those who join unsanctioned protests and launched criminal proceedings against some of the biggest leaders of the nascent anti-Putin movement.
The Russian leader's comments came shortly after a Moscow court ruled that a pair of fines slapped on the Golos independent polling agency for refusing to register as a foreign agent were valid.
Golos had been initially singled out by the authorities for doing polling during the election cycle and then chronicling alleged voting violations during the December 2011 parliamentary and March 2012 presidential polls.
Other outfits such as the highly respected Memorial human rights group that archives the atrocities committed in the Stalin era have also refused to sign up under the law and stopped receiving Western help.
Putin did not specify how he intended to improve the legislation but defended Russia's decision to monitor rights groups.
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