Although a growing number of businesses are expected to use search engine optimization (SEO) throughout 2009, a new report finds that Fortune 500 companies are struggling with the implementing the strategy.

While an outlook from Razorfish earlier in the week predicted that search engine optimization (SEO) will outpace paid search in 2009, a report today from Conductor finds that many Fortune 500 companies had low, or non-existent, visibility for the keywords they advertise most.

Seth Besmertnik, CEO of Conductor, says that many of these companies are just beginning to implement search engine optimization (SEO).

"SEO is still in its infancy for the Fortune 500. From quarter to quarter you can easily see when brands and sectors have become effective in managing natural search," he said. "We’re excited to be tracking the progress of these companies as the nascent search industry evolves."

One of the problems found in Conductor’s survey is that companies are spending too much money on the wrong keywords. According to Conductor, Fortune 500 companies spent about $51 million per day on 88,792 keywords, yet only 20.82 percent of those words show up in top 100 natural search results.