"I feel sorry for those who make such decisions as they cannot but understand that they are humiliating themselves," Putin said at an event in Moscow Thursday, according to Russia's state-run Tass news agency.
"The decision to suspend our Paralympians is beyond all boundaries of legal norms, moral principles and humanity.
"This is simply cynical to work frustration off on those who see sport as their sense to live, those who inspire with hope and belief millions of people with limited physical abilities."
When first announcing the ban, IPC president Philip Craven said the governing body had "enormous sympathy" for the athletes missing out on the Paralympics, but they had ultimately been failed by Russia's "medals-over-morals mentality."
Many in Russia disagree with Craven and the IPC, however, with a online petition
labeling the ban "inhuman" and calling for Russian athletes to be allowed to compete in Rio independently. It has received 300,000 signatures of support.
Several Russian disabled charities, including the All-Russian Society of Disabled People and the All-Russian Society of the Deaf, have also urged the IPC in an open letter
to reconsider its stance.
Kseniya Alferova, who helped start the petition, says she feels Russian Paralympians have been let down by the IPC and CAS.
"I'm friends with a lot of Russian Paralympians and their first reaction (to the CAS decision) is that they don't even want to talk, because they are so shocked," Alferova told CNN.
"The athletes are very strong, and I think some of them will recover. But I'm afraid some of them will not.
"It's a very difficult step for them, because they didn't believe in anything. Now they do. Now they have families, they believe in the future. And this is taking the future from them."
While 118 of the 389-strong Russian team were banned
from competing at this month's Rio Olympics due to the doping allegations, with individual federations given the responsibility for clearing athletes, the IPC implemented a blanket ban.
Alferova feels the Paralympians should have been handled differently.
"Everyone was sure the decision would be different," she said. "It has nothing to do with the country; it has to do with the people. The Paralympic Games are not countries, or politics -- it's people. It's not justice. It's not right."
The IPC has since responded to Alferova's petition, with spokesman Craig Spence stating that Russian Paralympians will not be allowed to compete independently from the Russian Paralympic Committee.
"Under the IPC's rules, one member is responsible for Russian athletes and that is the Russian Paralympic Committee," Spence said.
"It has been suspended due to its inability to fulfill its IPC membership responsibilities and obligations. If that member is suspended, then they cannot enter athletes into the Games."
Spence also echoed Craven's comments when adding that the athletes have been cheated out of a place at Rio by Russia's alleged doping violations.
"The athletes should be upset and angry with the officials behind this state-sponsored doping system in Russia," he told CNN.
"It is because of this system that the Russian Paralympic Committee is suspended. The system needs to change if the suspension is to be lifted."
Ludmila Bubnova, who was due to be part of Russia's first women's wheelchair tennis Paralympics team, believes an "unfair decision" from the IPC has cost her that dream.
"I couldn't believe it at first. I thought it was some sort of mistake," she told CNN. "I underwent doping tests so many times and was never caught up on anything. So why should I be banned from Paralympics if I don't dope?
"I think the decision was made with politics involved. It's an unfair decision. I believe that every athlete should be responsible for himself only. Why are you punishing innocent (people)?"
"My dream was to compete at the Paralympics. Sports means everything to me, I couldn't live without sport," Bubnova added. "We'll keep on training, we'll keep on fighting, we'll keep on playing -- it's life. Sport is our life."