The Global Ocean Commission, describing itself as an "independent high-level initiative on the future of the ocean," said current technology made the idea feasible and affordable.
Unique identification numbers and tracking devices are currently only required by passenger ships and large merchant vessels, while the commission said studies have suggested a link between the lack of unique identification and tracking technology and criminal activity such as people trafficking, illegal fishing and terrorism.
The 2008 Mumbai attacks in India, which killed more than 160 people, were carried out by attackers who reached the city aboard a private fishing trawler they commandeered, officials investigating the attacks said.
That kind of incident is exactly why a tracking system is necessary, the commission said.
"In the 21st century, when governments are doing so much to make their borders and citizens secure, it seems extraordinary that they have left a loophole big enough to sail a trawler full of explosives through," Commissioner Jose Maria Figueres said.
"For the security of citizens around the world, it seems clear that it is time to close the loophole."