Household names such as Pepsi, IKEA and Deutsche Bank were among companies named by the US-based International Consortium of Investigative Journalists (ICIJ) following a six-month investigation of 28,000 leaked documents.
The tax revelations risked weakening Juncker's position just days after he took office as head of the EU's executive arm after 19 years as Luxembourg prime minister, the period during which many of the deals were made.
Under an hour-long barrage of questions from reporters, the spokesman stressed that EU regulators were already investigating whether Luxembourg's deals with US Internet giant Amazon and the financial arm of Italian carmaker Fiat amounted to illegal state aid.
Spokesman Margaritis Schinas said that if the EU found it was in breach of the rules, "Luxembourg will have to take corrective actions." He added that the EU could widen the probe to companies mentioned in the ICIJ investigation.
Juncker presided over the tax affairs of Luxembourg for over two decades, transforming the country from a sleepy European backwater to a prized destination where hundreds of the world's biggest companies channel their affairs.
The leaks threaten to undermine his vow to be a more politically involved head of the European Commission, the EU's financial enforcer, especially as he is already embroiled in bitter rows with Britain and Italy over their budgets.
"These revelations are a major blow to the credibility of new commission president Juncker and his capacity to act for the public interest," said Sven Giegold of the Greens group in the European Parliament.
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