The Kremlin claimed he had officially held meetings since 5 March and released photos and videos of him on national television, but Russian media reported the images had been taken much earlier.
Last week, he postponed a trip to Kazakhstan fuelling speculation that he was unwell.
His absence also sparked other rumours, including a theory he had been overthrown by security agencies in a coup or another reported by a Swiss newspaper that he had travelled to Switzerland after his alleged girlfriend had given birth to their baby.
Commenting on the rumours, spokesman Dmitry Peskov said: “So, have you seen the president paralysed and seized by the generals?
“He has just come back from Switzerland where he attended the delivery.”
Putin prides himself on his macho image as Russian leader, and said in 2008 he worked “like a galley slave” to run the country.
It comes after he launched a massive military exercise involving 40,000 servicemen in the Arctic.