Fewer than 12,000 of 100,000 companies examined actually have a presence on the Web, the survey found.
Of those that do have a website, many omit key features such as prominent contact information or links to social media sites, while others were not optimised to be found by search engines.
"For companies that have made the effort to get online, the majority of them have a substandard Web presence," said Andrew Thomas, the managing director of Local Media.
The survey of 11,812 websites belonging to small and medium-sized enterprises in the UAE was conducted for Local Media by the digital media firm vSplash, based in the United States. It took 90 factors into consideration when evaluating the sites.
"Many sites didn't have a contact form or they didn't have a telephone number, or it was difficult to find," said Mr Thomas.
The survey found that 90 per cent of the sites had no links to social media platforms, 80 per cent had no local address listed, and many were not optimised for viewing on smartphones.
"The way that people search for information is changing. You're not picking up a Yellow Pages book any more and looking for something - you're getting online," he said.
"But if you have the wrong presence, it can probably do more harm than good."
Local Media runs a site called Local Search, which launched in October last year and has listings for 125,000 companies in the UAE.
Another arm of business specialises in website development, strategy and shooting videos for online use.
The importance of social media was underlined by a separate study by eMarketer, in collaboration with Starcom MediaVest Group.
It found that 70.2 per cent of internet users in the Middle East and Africa will use social media  this year. Social networking is growing faster in this region than anywhere else, the report found.