Regulators had expressed concerns that the two companies could be colluding, especially since Google is now making phone software.
However, the FTC's Bureau of Competition said in a statement today that will continue to investigate links between the two companies.
"We have been investigating the Google/Apple interlocking directorates issue for some time, and commend them for recognising that sharing directors raises competitive issues, as Google and Apple increasingly compete with each other," said Bureau of Competition director Richard Feinstein.
"We will continue to investigate remaining interlocking directorates between the companies."
The term 'interlocking directorate' refers to the practice of one person serving on the boards of two, usually competing, companies. Feinstein is likely to be referring to Genentech chairman Arthur Levinson, who joined the boards of Apple in 2000 and Google in 2004.
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