Guenther Oettinger has said he took the lift because he would otherwise have arrived late for a planned meeting with Hungarian Prime Minister, Viktor Orban.
But critics accuse him of breaking European Union rules against accepting gifts of more than €150 (£129).
Mr Oettinger was already facing criticism after using an offensive term about Chinese people in a speech.
The flight took place on 18 May this year when Mr Oettinger was going to a conference in Budapest about the future of the car industry.
He was due to meet Mr Orban the night before, and - unable, he says, to make it to the meeting any other way - accepted a lift in the private jet of Klaus Mangold, a German businessman who is a former manager at the Daimler luxury car company.
But the worldwide anti-corruption charity Transparency International told German media (in German) that Mr Mangold is also a lobbyist with close connections to Russia's President Vladimir Putin.
Under EU rules, contact with lobbyists must be declared.
Daniel Freund of the group's Brussels office said: "All commissioners can access business class flights and a fleet of jets, so it is unclear why Mr Oettinger accepted this invitation."
The embattled commissioner tweeted on Tuesday that the allegations were "unfounded" and that the Hungarian government had suggested that he take Mr Mangold's plane.
But the head of the Greens in the European Parliament, Rebecca Harms, said Mr Oettinger had to face some "very uncomfortable questions".
She said: "It is very alarming that an EU commissioner can let a lobbyist close to the Kremlin fly him across Europe, and can find that totally normal."
As well as representing Germany at the European Commission, Mr Oettinger holds the portfolio for digital economy and society.
Earlier this month he apologised for comments in which he spoke of Chinese officials having "hair combed... with black shoe polish" and called them "slitty-eyed".
Germany's EU commissioner is under fire for accepting a trip to Hungary in a Kremlin-linked lobbyist's private jet.