At-risk species, including wolves and sharks, are being targeted by hunters using signals sent by radio tags to home in on the animals.
The behaviour of non-endangered species is also being skewed as nature fans use the signals to get close to wild animals, say biologists.
A group of scientists has now begun collecting evidence to measure how tagged species are being harmed.
They are calling for changes to tagging systems to make them harder to abuse.
Hunting and fishing
Prof Steven Cooke, a biologist at Carleton University in Canada, said growing numbers of scientists who use tagging were getting increasingly worried about the "unintended consequences" of the technology.
"We go out and do the science and provide the information and assume all is good but there are many ways in which this process can be corrupted," Prof Cooke told the BBC.
Tagging with transponders that communicate via satellite or radio was becoming an increasingly common way to study species, he said, and had produced "incredible" insights into the movements and lifestyles of many different creatures.
In some cases, he said, tags were used to keep an eye on small populations of endangered animals but there were also many cases in which tagging was used on a much more ambitious scale.
For instance, he said, more than 100,000 tagged fish were released in to the Columbia River basin every year to help monitor fish stocks, movements and migration patterns. The Great Lakes were also home to more than 5,000 tagged fish, he added.
Many different groups of people were interested in using the signals sent out by tags to locate all kinds of animals, said Prof Cooke.
A paper co-written by Prof Cooke and other biologists for the Conservation Biology journal detailed some of the "troubling" ways in which tags had become an inadvertent aid to poachers, hunters, photographers and nature lovers.
"This is not something that a lot of papers have been written on," he said. "We found a lot of the examples by searching on the net and on news sites and less traditional sources."
Examples gathered by the scientists included:
- sharks tagged during a conservation programme in western Australia were found and then killed by people homing in on radio signals
- attempts by poachers in India to hack GPS data sent by collars on Bengal tigers
- commercial fishing vessels using radio data to find fish known to feed near the species they want to catch
- efforts by "wolf-persecution" groups in the US to decode signals to help them hunt down the predators
Some national parks had taken steps to limit abuse by banning the radio receivers that can pick up the "beeps" sent out by some types of tag, said Prof Cooke.
As a result of the paper, other biologists shared information about other ways tagged animals were being targeted, he said.
Prof Brendan Godley, director of the centre for ecology and conservation at the University of Exeter, said the lifestyles of some species made it easier to abuse tag data.
Knowing the approximate location of a shark, he said, would help track it down as they were likely to respond to lures, such as baited lines or food trails, put in the water close to them.
By contrast, he said, other species may be far harder to find, despite being tagged, because they did not respond in the same way.
Prof Godley added that tagging had an impact far beyond improving our understanding of how animals live.
Tagging can directly contribute to conservation efforts and make them much more effective, he said.
"Within two weeks of tagging leatherback sea turtles we were able to show that the marine park that was set up for their benefit was inadequate," he said.
Data provided by tagging showed which locations fishing fleets were told to avoid when turtles were nearby.
However, he added, it was clear that tagging had become a contentious issue that had to be tackled.
"Scientists need to do a better job of getting the public aware of why they are doing the research and we need to do a better job of sharing the dividends of our work," he said.