Last week, The TES revealed plans to embed the radio-frequency ID chips in the clothes of 36 autistic pupils, which would let local leisure centre staff know when they passed scanners.
Doncaster Education City, a 14-19 education partnership, was set to spend about pound;10,000 of a Learning and Skills Council grant on the technology.
Bill Webster, acting principal of Doncaster College, only learnt of the education partnership's plans through The TES. "We would be wary of any form of technology that would have negative data protection implications," he said.
Doncaster College is the second school to pull out of a trial. Nearby Hungerhill School terminated a pilot this term after it emerged that the technology would be marketed commercially.
Moves are still in place to run a trial at a school in Croydon. Mary Turner, a school governor there, said the technology would allow teachers to keep track of pupils' behaviour and academic progress.
Trevor Darnborough, managing director of Darnbro Ltd, which embroiders the chips into school uniforms, said they posed no threat to pupils' civil liberties.
"The only tracking our system can perform is to tell us what class they were in last - even the old registration book did that," he said. "Does that fall foul of civil liberties? If it does, we live in a sad world. I always thought that pupils' whereabouts and safety were of paramount importance.
"The microchip used is exactly the same as a door-entry swipe or bank card ... You can't be tracked by those in real time."