Pichai, a 43-year old from India, faces the task of improving attitudes towards Google in Europe, where national governments are pushing the EU to take a closer look at its dominance of the search engine market.
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A spokesman for Vestager confirmed the meeting, but refused to provide any further details of what was discussed.
European competition officials have been investigating the US tech giant for years over alleged monopolistic practices involving its search engine but a solution has been elusive.
Google is also under fire in Europe for paying extremely low taxes through the use of complex cross-border financial arrangements.
This was the first meeting between Competition Commissioner Vestager and Pichai, the new CEO of Google, and follows a meeting last March with Eric Schmidt, the company's chairman.
Three successive proposals by Google for an amicable settlement have been rejected and last year Vestager sent the company a "statement of objections" over its online shopping services.
It said Google had diverted traffic from rival price-comparison services like Kelkoo, which operates in several European countries, to favour its own product.
Google responded in late August that Brussels's findings were wrong and based on a flawed evaluation of the market.
If no agreement is reached and the group is found to have broken EU anti-trust rules, it could face fines amounting to billions of dollars. A decision is expected before this summer.
In addition to the initial investigation into Google's search engine which began in late 2010, the European competition service opened a second probe in April to examine the group's Android mobile operating system.
This software, used by a wide range of brands, is installed in more than 80% of the world's smartphones.
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