The supermodel, who questioned Mr Putin for GQ magazine, avoided political subjects but chose to talk about the prime minister's fitness regime and a glamour calendar produced in his honour.
The model, who lives with Russian billionaire Vladislav Doronin in Moscow, asked: "You're in pretty good physical shape. How do you manage to keep yourself so fit?"
Mr Putin, who is often photographed taking part in macho pursuits, said he did not work out as much as he should, but goes to the gym, swims every day, and "from time to time" meets with friends and does "extra-curricular stuff".
Naomi, 40, asked how the prime minister felt about a group of students who posed in lingerie for a calendar to mark his 58th birthday.
She said: "You obviously make a great impression on women. How do you feel about the students who posed for you in the calendar?"
Mr Putin said the "girls in the erotic calendar were courageous" for showing open support.
But he hit back at a rival calendar, where the young women posed in black with their mouths taped shut.
He said: "In almost any country, probably in Russia in particular, it's fashionable to criticise people in power."
Naomi, who interviewed Venezuelan leader Hugo Chavez in 2008, also asked Mr Putin about his liking for extreme sports, motorbikes and bare-knuckle fighting