Viviane Reding told the BBC that authorities found that "transparency rules have not been applied".
The policy change, implemented on Thursday, means private data collected by one Google service can be shared with its other platforms including YouTube, Gmail and Blogger.
Google said it believed the new policy complied with EU law.
It said the new set-up would enable it to tailor search results more effectively, as well as offer better targeted advertising to users.
It went ahead with the changes despite warnings from the EU earlier this week.
Data regulators in France had cast doubt on the legality of the move and launched a Europe-wide investigation.
More than 60 sets of guidelines for its individual Google-owned sites were merged into a single policy for all of its services.
It means browsing data and web history, which is gathered when a user is signed in with a Google account, can be shared across all of the websites.
Google's business model - the selling of ads targeted on individual user behaviour - relies on collecting browsing information from its visitors.
Until Thursday, different services did not share this information.
This meant a search on, for example, YouTube, would not affect the results or advertising you would encounter on another Google site such as Gmail.
The new agreement, which users cannot opt out of unless they stop using Google's services, will mean activity on all of the company's sites will be linked.
Logging out of Google's services will reduce the amount of data stored by the company, although - like many other sites - it will still store anonymous data about web activity.
France's privacy watchdog CNIL wrote to Google earlier this week, urging a "pause" in rolling out the revised policy.
"The CNIL and EU data authorities are deeply concerned about the combination of personal data across services," the regulator wrote.
"They have strong doubts about the lawfulness and fairness of such processing, and its compliance with European data protection legislation."
The regulator said it would send Google questions on the changes by mid-March. On Thursday, Ms Reding told BBC Radio 4's World At One that conclusions from initial investigations had left CNIL "deeply concerned".
'Strong as ever'
Earlier, Google's global privacy counsel Peter Fleischer said he was happy to answer any concerns CNIL had.
"As we've said several times over the past week, while our privacy policies will change on 1st March, our commitment to our privacy principles is as strong as ever," Mr Fleischer wrote in a blog post.
The company rejected the regulator's request to hold off on making the changes. Users are being moved on to the new single policy shortly after midnight on 1 March, local time.
Many websites and blogs in the technology community have given guidance for users concerned about how their browsing history will be used.
They suggest users can access, and delete, their browsing and search history on the site by logging in togoogle.com/history.
A similar page for YouTube viewing and search historycan also be accessed.
Users can see which Google services hold data about them byviewing their dashboard.
In preparation for the policy change, Google displayed prominent messages notifying visitors about the plans. A dedicated section was set up toprovide more details.
However, campaign group Big Brother Watch has argued that not enough has been done to ensure people are fully aware of the alterations.
A poll of more than 2,000 people conducted by the group in conjunction with YouGov suggested 47% of Google users in the UK were not aware policy changes were taking place.
Only 12% of British Google users, Big Brother Watch said, had read the new agreement.
The group's director Nick Pickles said: "If people don't understand what is happening to their personal information, how can they make an informed choice about using a service?
"Google is putting advertisers' interests before user privacy and should not be rushing ahead before the public understand what the changes will mean."