All 10 passengers aboard the plane were reported dead.
In a televised speech on Thursday, Putin said he was told about the plane crash “this morning”.
He extended his condolences to the victims’ families, saying Prigozhin “was a talented businessman”.
The Russian president said investigators would look into what happened but added that it would take time.
United States President Joe Biden had said he was not surprised that the leader of the Russian mercenary group may have been targeted.
Prigozhin had led a failed uprising against Putin in a move analysts said was the biggest threat to the Russian president’s rule since he assumed power in 1999.
Putin described the mutiny as a “stab in the back” vowing that the organisers would face justice.
Earlier in July, Biden had said Prighozin should be worried about his safety following the failed mutiny.
Speaking further on the Wagner leader’s reported death, the US president said “not much that happens in Russia that Putin is not behind but I don’t know enough to know the answer”.
Adrienne Watson, US national security spokesperson, also said Prighozin’s death was not a surprise given his history with Putin.
The mercenary leader’s last reported location appeared to be in Africa when he posted his first video address since his rebellion in Russia.
