The furore comes just days after the official, who is in charge of the digital agenda portfolio, was caught in a row over allegedly derogatory comments he made about Chinese people.
The latest revelations concern a journey he made on 18 May on the private jet of Klaus Mangold, a German businessman said to be close to Moscow, at the invitation of Austrian construction firm Strabag.
Mangold has advocated lifting EU sanctions on Russia and is Vice-Chair (Europe) of investment bank Rothschild.
He has connections to both the Kremlin and Hungarian government, and works as a consultant for a multi-billion euro nuclear project known as Paks II.
After flying to the Hungarian capital in May, Oettinger met with Hungarian Prime Minister Viktor Orbán. However, the Commissioner denies having discussed the Paks nuclear power plant, a controversial project in which Orbán has been at odds with the EU over plans to build two Russian reactors.
According to the Commission's code of ethics, Commissioners cannot accept gifts worth more than €150.
It is not the first time the German, a former energy Commissioner, has hit the headlines.
He recently also found himself in the spotlight over comments about Chinese diplomats and gay marriage, among other things.
After reportedly calling Chinese "slitty eyes", he was later forced to apologise about comments he made in a speech he gave in Hamburg, saying, "I had time to reflect on my speech, and I can now see that the words I used have created bad feelings and may even have hurt people.
"This was not my intention and I would like to apologise for any remark that was not as respectful as it should have been."
After the latest revelations came to light earlier this week, Oettinger has faced some calls from critics to resign.
Oettinger was recently named as the honorary consul in Russia of Germany's Baden-Wurtemberg, his home region.
In a tweet, he rejected the criticism, saying, "The allegations are unfounded."
On Thursday, the Commission stood by him, saying that his flight with Mangold in May was not a meeting that fell under EU ethics and transparency rules.
The Commission said that the flight was not a gift but a "means of transport" and that it was offered by a government, not a lobbyist.
Commission chief spokesperson Margaritis Schinas, speaking in Brussels on Thursday, said, "Oettinger had to opt for this type of transport as he received an invitation to meet one of the 28 heads of state of government, and the only possible way to do it was to accept the invitation from the Hungarian government offered him this specific kind of transport.
"This would not be seen as a conflict of interest and this is within our norms."
The trip with Mangold had been arranged by the Hungarian government and, since the meeting with the German businessman had not concerned Oettinger's digital portfolio it had not been necessary to record it in the Commission's lobbying register, he said.
In Hungary, the Prime Minister's chief of staff, Janos Lazar,also said Oettinger had done nothing wrong and defended the Hungarian government's position, telling reporters that it was Mangold who recommended to the Hungarian authorities to organise a conference Oettinger attended during his May visit.
Despite the robust defence of the official by the Commission, Vicky Cann, of the Corporate Europe Observatory, remained critical.
"The Commission's interpretation of the transparency rules is ludicrous."
The Commission on Thursday ended one investigation into the Paks II plant, closing an infringement case against Hungary on EU public procurement rules.
The case was opened a year ago because Hungary did not hold an open tender when it hired Russia's Rosatom to expand the plant. However, another Commission investigation is still ongoing on possible illegal state aid in the Paks II case.