A letter issued by the Article 29 Working Party, a group of EU privacy regulators, warned the three companies that their "methods of making users' search data anonymous" were out of step with the EU's rules on data protection.
The regulators sent copies of these letters to the US Federal Trade Commission (FTC) and to Viviane Reding, vice-president of the European Commission responsible for justice, fundamental rights and citizenship.
The letter asked the US authorities to see if the search engines' use of search data complied with their own Federal Trade Commission Act, which prohibits "unfair or deceptive practices".
The regulators specifically take aim at Google's nine-month retention rate of its search logs, which compile data from users' search queries.
The Working Party asks Google to cut the retention period from the current nine months to six months.
"The company's apparent lack of focus in data retention is concerning," according to the statement.
"Considering Google's dominant position in almost every EU member state, with a market share of up to 95% in some national search engine markets, the company has a significant role in European citizens' daily lives," the letter continued.
The group is also insisting that the company must get an outside auditor to assess how anonymous users' data actually was.
Google said it has not received the working party's letter but issued a statement insisting that the company needed to keep the data for nine months in order to make searches both safer and more relevant.
"We develop our policies based on what provides the best experience for users both in terms of respect for their privacy and the quality and security of our services. Our current retention policy represents the most responsible balance between these two important concerns," reads a statement from the company.
Last week, Google was also in the EU's line of fire for inadvertently collecting Internet users' personal data via wireless receivers installed in cars that provide the images for its street mapping service, StreetView (EurActiv 21/05/10).
Under pressure from regulators in January, Microsoft announced it would delete the entire IP address from search queries after six months.
In response to the working party's letter, Thomas Myrup Kristensen, the company's senior EU policy director, said Microsoft looked forward to continued dialogue with the body and encouraged the EU "to ensure that the whole search market, including the 95% that in some markets is held by a single company, is held to a single standard".