European Commission President Jean-Claude Juncker was thrust to the center of a global debate on corporate tax havens following the release of thousands of secret documents detailing how Luxembourg, the country he led for nearly 20 years as prime minister, helped companies avoid paying taxes.

The documents, disclosed by the Washington-based International Consortium of Investigative Journalists on Thursday, provide fresh detail on how hundreds of the world’s biggest companies, including PepsiCo Inc., FedEx Corp. and Amazon.com Inc., have funneled profit through subsidiaries in Luxembourg, avoiding billions in taxes in other jurisdictions.

The revelations come less than a week after Mr. Juncker took over Europe’s top office and threaten to cast a shadow over his campaign to move the 28-member European Union beyond the political and economic travails that have hobbled it in recent years. All of the tax deals described in the documents, which run until 2010, were granted during Mr. Juncker’s time as Luxembourg’s leader.

“I expect Mr. Juncker, who served for 20 years as Luxembourg’s prime minister and finance minister, to provide details of how Luxembourg’s tax authorities operate,” Carsten Schneider, a senior member of Germany’s Social Democrats, said during a heated parliamentary debate on Thursday.

The main question Mr. Juncker faces in the short term is how he can demand continued belt tightening in countries such as Greece and Portugal, when his own country is helping companies avoid paying taxes across Europe. Even as much of Europe has been stuck in an economic funk, Luxembourg has prospered.