Mahathir said he doesn't think the findings of the international investigative team "is true at all" as it was based on hearsay.
"We are very unhappy because from the very beginning, it became a political issue on how to accuse Russia of the wrongdoing," he told reporters. "Even before they examine (the debris), they already say Russia. So it is very difficult for us to accept that."
In announcing the charges Wednesday, prosecutors appealed for witnesses to help lead them even further up the chain of command in President Vladimir Putin's Russia.
Russia's Foreign Ministry called the charges against its citizens "absolutely unfounded" and accused the investigators of using "dubious sources of information" and ignoring evidence provided by Moscow in order to discredit Russia.
Malaysia Airlines Flight 17 from Amsterdam to Kuala Lumpur was brought down on July 17, 2014, over eastern Ukraine by what investigators said was a Buk missile from a Russian anti-aircraft unit. Investigators believe the Ukrainian rebels probably mistook the Boeing 777 passenger jet for a Ukrainian military plane.
Eastern Ukraine's pro-Moscow rebels have relied heavily on Russian military assistance during the separatist conflict that erupted in April 2014 and has claimed more than 13,000 lives.
"As far as we are concerned we want proof of guilt ... but so far, there is no proof. Only hearsay," Mahathir said. "I hope everybody will go for the truth."
Malaysia's Foreign Ministry said the country remained committed to the investigation to ensure it remains transparent, credible and effective. It urged all parties to cooperate with the process.
In Australia, Paul Guard, the son of MH17 passengers Roger and Jill Guard, told the Australian Broadcasting Corp. that he's glad the investigation has progressed and nearing its end. But he said he doesn't hold out much hope that the four men charged will face court.
The parents of another victim, Jack O'Brien, who was one of 38 Australians on the plane, said it was hard for them to even look at the photos of the suspects.
"I also looked at the faces of the ... average soldiers from that brigade and wondered, you know, are any of them remorseful for what's happened if they played a role? Who knows. We don't know them, we don't know what their lives are."
One of those charged was Igor Girkin, a retired colonel in Russia's main intelligence agency, the FSB. He led Russian and separatist forces in Ukraine's Donetsk region in 2014.
Girkin dismissed the accusations in a telephone interview Wednesday, saying the "insurgents did not shoot down the Boeing." Girkin lives in Moscow.
The three others charged are Russian citizens Sergey Dubinskiy, identified as a former employee of Russia's military intelligence service, and Oleg Pulatov, described as a former soldier in military intelligence; and Leonid Kharchenko, a Ukrainian citizen who led a combat unit in the Donetsk.