Reports on the irregularities “are very concerning and give rise to questions regarding the compliance with EU law," European Commission spokeswoman Anitta Hipper was quoted as saying.
In response to the allegations, EU Home Affairs Commissioner Ylva Johansson has penned a letter to Polish authorities, seeking "clarifications," and expects a response by October 3, Hipper added.
Warsaw has dismissed the notion of the "visa fraud scandal" being widespread as "absurd."
On Tuesday, Germany's foreign ministry summoned Poland's envoy to Berlin to address inquiries about the allegations.
Poland's security service has disclosed that seven individuals had been apprehended in connection to the alleged scandal.
The Gazeta Wyborcza newspaper, which is critical of the government, claimed last week that Poland's foreign ministry might have allowed hundreds of thousands of migrants to come to Europe.
A system was allegedly established for granting Schengen visas to individuals from the Middle East and Africa in exchange for financial considerations, involving both Polish consulates and certain external companies in the countries concerned.
The scam has come as an awkward blow for a government that has made controlling immigration central to its campaign for Poland's mid-October general election, news outlets reported.