The civil rights office of the Department of Health and Human Services opened the investigation on Tuesday, The Wall Street Journal reported.
The office "will seek to learn more about this mass collection of people's medical records to ensure that [the Health Insurance Portability and Accountability Act of 1996 or HIPAA] protections have been fully implemented," Office Director Roger Severino said in a statement to the publication.
The Department of Health and Human Services did not respond to a request for comment from CNN Business.
Data collection is being done through a new partnership between Google ( GOOG ) and the Ascension, one of the largest non-profit and Catholic healthcare systems in the country . The two companies have confirmed that they are working together to analyze patient data and are giving healthcare professionals new insights and suggestions about patient care. The Wall Street Journal was the first report on the project on Monday.
The Google-Ascension partnership will integrate into the cloud the various areas of Ascension health data. Google said in a blog post on Monday that the project is "a business contract to assist a provider with the latest technology, similar to the work we do with dozens of other healthcare providers."
The magazine has at least 150 employees Google had access to patient data, but Google said it adhered to regulatory standards such as HIPAA. Google said that Ascension data "cannot be used for any purpose other than to provide those services we offer under the agreement, and patient data cannot and will not be combined with any data for Google users."  Shortly after the journal report was published, both companies released statements.
Google acknowledged the sensitive nature of patient health data. Ascension, based in St. Louis, has 2,600 facilities in approximately two dozen states. He said his partnership with Google follows the law. However, the magazine reports that some Ascension employees have doubts about how Google shares and collects patient data.
This is not the first time Google has encountered control over user data processing.
Google paid a record $ 170 million in damages to the Federal Trade Commission to settle allegations that YouTube violates the law when it deliberately tracks and sells ads targeting children.
Google's googling for healthcare comes amid growing interest in space from technology companies such as Apple ( AAPL ) Amazon ( AMZN ) and Microsoft ( MSFT ) . All three companies have launched initiatives to modernize the US healthcare system in recent years.
Rachel Mets and Jordan Walinski contributed to this report.