Crash investigators have still to conclusively identify the remains of the 10 people believed to have died in Wednesday's crash northwest of Moscow, and Putin said the examination would take time.
"As for the aviation tragedy, first of all I want to express my most sincere condolences to the families of all the victims. It's always a tragedy," Putin said in televised remarks made during a meeting in the Kremlin with the Russian-installed chief of Donetsk region in eastern Ukraine.
"Indeed, if employees of the Wagner company were there, and the preliminary data indicate they were, I would like to note that these people made a significant contribution to our common cause of combating the neo-Nazi regime in Ukraine, we remember this, we know it and we shall not forget," he added.
The crash occurred exactly two months after Prigozhin led a mutiny against Russia's army leadership, a act of rebellion that Putin at the time condemned as a treacherous "stab in the back".
Putin on Thursday recalled that he had known Prigozhin - a convicted criminal who went on to establish a successful catering company before founding the Wagner mercenary group - since the early 1990s, in the immediate aftermath of the collapse of the Soviet Union.
"He (Prigozhin) was a talented person, a talented businessman, he worked not only in our country, and achieved results but also abroad, particularly in Africa. He was involved there with oil, gas, precious metals and stones," Putin said.
"He was a man of a complicated fate. He made some serious mistakes in his life but he also achieved the needed results," he added.
Russian investigators opened a criminal probe but there has been no official word on what may have caused Wednesday evening's crash.
Until Putin's comments there had been no official confirmation of Prigozhin's death beyond a statement from the aviation authority saying he was on board.
Prigozhin, 62, was head of the Wagner mercenary group and a self-declared enemy of the army top brass over what he said was its incompetent prosecution of Russia's war in Ukraine.
State media gave the plane crash low-key coverage.
The Embraer Legacy 600 executive jet, which had been flying from Moscow to St Petersburg and was reported to have also been carrying senior members of Prigozhin's team, crashed near the village of Kuzhenkino in the Tver region north of Moscow.
A Reuters reporter at the crash site on Thursday morning saw men carrying away black body bags on stretchers.
Part of the plane's tail and other fragments lay on the ground near a wooded area where forensic investigators had erected a tent.
The Baza news outlet, which has good sources among law enforcement agencies, reported that investigators were focusing on a theory that one or two bombs may have been planted on board.
Prigozhin spearheaded the mutiny against the army leadership on June 23-24 which Putin said could have tipped Russia into civil war.
The mercenary leader also spent months criticising the conduct of Russia's war in Ukraine - which Russia calls a "special military operation" - and had tried to topple Defence Minister Sergei Shoigu and Valery Gerasimov, chief of the General Staff.
The mutiny was ended by an apparent Kremlin deal in which Prigozhin agreed to relocate to neighbouring Belarus.
But he had appeared to move freely inside Russia.
with DPA
