The move comes after AOL accidentally released information on 20 million private search records, before removing the data and apologising for its actions.
The privacy group is also urging the FTC to require AOL to notify customers affected by the disclosure, and to stop logging search data except when absolutely necessary.
"Search terms can expose the most intimate details of a person's life: private information about family problems, medical history, financial situation, political and religious beliefs, sexual preferences, and much more," said EFF staff attorney Marcia Hofmann.
"At the very least, AOL should notify every customer whose privacy has been jeopardised by the company's careless handling of this incredibly private information, and AOL should not store this kind of data in the future when it does not have to."
The EFF is also trying to track down AOL customers affected by the leak, urging them to contact the online media giant and ask whether their data was released.
"We have asked the FTC to make sure that AOL rectifies the damage and improves its privacy protection for the future," said EFF staff attorney Kevin Bankston.
"But this problem is not limited to AOL, because every search company stores this kind of data.
"Hopefully, AOL's shocking violation of its users' privacy will spur Congress to clarify that the same law that prevents these companies from disclosing personal emails also applies to search logs."
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