The famously macho politician, 58, seemed to be wearing heavy make-up when he was photographed with a dark patch around one eye on a visit to Ukraine.
Some suggested Russia’s best-known black belt had suffered a judo injury.
But his office denied the mark was a bruise, putting his looks down to a busy schedule and poor lighting.
“Ukrainian, Russian and Western journalists… talked only of one thing – how did the Russian prime minister get a bruise under his eye?” wrote Andrei Kolesnikov, the Kremlin correspondent for Russia’s Kommersant business daily.
“Could it really be the result of some tough sparring? It may have been carefully covered up, but nobody could fail to notice it.”
Mr Putin arrived for his talks with Ukrainian leaders in a “bad mood” and with “something like a big bruise on his left cheekbone”, according to Ukrainian television channel TCH.
“He also had on his face a very noticeable swelling… badly covered up with make-up,” it added.
According to the Associated Press news agency, the news conference in Kiev was cut short and a planned dinner was cancelled.
Mr Putin’s face looked normal when he was photographed in Moscow on Tuesday, suggesting the change in his appearance occurred within the following 24 hours.