Snowden, writing in Britain's Guardian newspaper, said he was taken aback at criticism of his decision to take part in the show during which Putin greeted him, to laughs from the audience, as a fellow "former agent".
Snowden asked Putin: "I'd like to ask you: does Russia intercept, store or analyse in any way the communications of millions of individuals?"
Putin replied: "We have strict legal regulation of the use of special surveillance by special services, including tapping phone conversations, surveillance on the Internet and so on," Putin said.
Snowden, who appeared via video-link, said in the article that Putin "denied the first part of the question and dodged on the latter".
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The man behind the US National Security Agency leaks said he was surprised "that people who witnessed me risk my life to expose the surveillance practises of my own country could not believe that I might also criticise the surveillance policies of Russia, a country to which I have sworn no allegiance, without ulterior motive".
Even some of Snowden's supporters have criticised his involvement in the Putin phone-in. Snowden was granted asylum by Russia last August after rocking the US intelligence establishment with his leaks.
"But to me, the rare opportunity to lift a taboo on discussion of state surveillance before an audience that primarily views state media outweighed that risk," he wrote.
"Moreover, I hoped that Putin's answer - whatever it was - would provide opportunities for serious journalists and civil society to push the discussion further.