Putin, who was in London for talks with British Prime Minister David Cameron and to take in some Olympic events, offered his first reactions to the trial on Thursday.
The Russian leader emphasized he felt the band's anti-Putin stunt at Moscow's Christ the Saviour Cathedral in February "was no good," and noted that had the group staged it elsewhere, the outcome might have been even more serious.
"If the girls were, let's say, in Israel, and insulted something in Israel ... it wouldn't be so easy for them to leave," he said. "If they desecrated some Muslim holy site, we wouldn't even have had time to detain them."
That said, he concluded he felt the Russian court should show the women leniency.
"I don't think they should be judged too severely for this," Putin said.
"But the final decision rests with the courts — I hope the court will deliver a correct, well-founded ruling."
In February, ahead of Putin's contentious return to the Russian presidency for a third term, Pussy Riot took over the pulpit of Moscow's main cathedral to perform what the band described as a "punk prayer" decrying the leader and the church's support of him.
Clad in brightly coloured outfits and balaclavas, the feminist band's members danced and sang lyrics that included "Virgin Mary, drive Putin away!" The incident reportedly lasted less than a minute before security led the women out.
Three band members — Nadezhda Tolokonnikova, 23, Maria Alekhina, 24, and Yekaterina Samutsevich, 29 — have been detained since February, charged with hooliganism motivated by religious hatred.
Their trial began on Monday and they face up to seven years in prison if convicted. The trio issued a not-guilty plea and the women have argued they were staging a political protest.
This week, also timed to Putin's visit to London, top musicians including Pete Townshend, Jarvis Cocker and Corinne Bailey Rae called for the release of the detained Pussy Riot members, and urged Putin to ensure the women receive a fair hearing.