Speaking at an economic forum in the eastern city of Vladivostok, Putin appeared to deny that they worked for Russia's military intelligence service the Main Directorate, commonly called GRU.
British authorities said the two men, who they identified as Alexander Petrov and Ruslan Boshirov, had been operating under aliases.
On March 4, Skripal and his daughter were found slumped unconscious on a bench in Salisbury after being exposed to the nerve agent Novichok.
Britain has said the two suspects were Russian military intelligence officers nearly certainly acting on orders from high up in the Russian state. "We'll see in the near future".
The Skripals spent weeks in hospital in a critical condition after the poisoning.
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Russian Federation has said the names of the suspects - as indicated in their passports - given to them by British prosecutors were meaningless.
The statement by Putin marked an abrupt shift from Russia's earlier position on the poisoning case that has damaged relations between Moscow and the West.
They believe the men smeared the highly toxic chemical Novichok on a door handle at the Wiltshire home of Mr Skripal.
Putin said they were civilians who did not work for the military.
"We have repeatedly asked Russian Federation to account for what happened in Salisbury in March and they have replied with obfuscation and lies", Slack said.
The poisoning led Britain, the United States, the European Union, and others to carry out a series of diplomatic expulsions and financial sanctions against Moscow.
It has further damaged already severely strained relations between Russian Federation and the West and has been a cause for solidarity at a time when Western officials accuse Moscow of seeking to cause rifts in relations between Western countries.