The FTC, which sent the letters on Monday, has the power to fine companies that violate its rules against deceptive advertising.
The agency said background shading for search ads that appear alongside natural search results was not always sufficiently visible, particularly on mobile devices.
Text labels intended to flag search ads were not always easy to spot, as some search engines had reduced the font size of the text or placed a single label at the corner of a group of ads.
In the case of voice-based search for instance, the agency said that a search engine should make an "audio disclosure that is of an adequate volume and cadence for ordinary listeners to hear and comprehend it."
(Read More: Google 'Putting Consumers at Risk,' State AGs Say)
The letters, which were also sent to several popular "vertical" search engines that specialize in online shopping, travel and local business, did not specifically accuse any search engines of wrongdoing.
Google, the world's No.1 search engine, accounted for 73.8 percent of the $17.3 billion spent on search advertising in the United States last year, according to research firm eMarketer. Last year Google altered its specialized shopping search engine, making it based solely on paid search listings.
Google said in a statement that clear labeling and disclosure of paid search were important and "we've always strived to do that as our products have evolved."
Yahoo, which had 6.6 percent share of the U.S. online search ad market in 2012 according to eMarketer, said it was reviewing the letter and stressed its commitment to a transparent search experience.
Microsoft, the No.3. online search advertising company in the United States, declined to comment.