This is the second raid in five weeks, with the company's offices in Paris being raided on May 24.
The Madrid raid comes after the EU announced a third set of anti-trust charges against the search behemoth.
Google is headquartered in Ireland which has a low rate of corporate tax and it has been criticised in several countries, including Australia, for not paying its fair share of tax.
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Earlier this year, the company agreed to pay £130 million in Britain to make up for evading taxes for more than a decade.
Apart from the tax raids, Google faces problems on other fronts with reports that the EU will hit the company with a massive €3 billion fine for using unfair tactics to dominate the search engine market.
Google is not the only company to be under scrutiny for non-payment of tax; last year the chief executives of Google, Microsoft and Apple appeared before an Australian Senate committee.
Under examination were the complicated tax structures these companies have and also the reasons why they refuse to pay their fair share of tax for doing business in Australia.
Criticism of the company is not limited to the tax area. Recently, a senior research psychologist Robert Epstein listed the ways in which Google uses its power in the search realm to twist things to benefit itself.