The department placed a ban on an Iraqi immigrant, known only as AE, from taking AS-level courses in chemistry and human biology.
It claimed that the information provided as part of the course could be used to implement terrorist activities.
AE is in his mid-thirties and unemployed. He studied medicine before coming here and is suspected of having terrorist affiliations. So he has been placed under a government control order limiting his freedom and activities.
AE has been under the order since 2006, making it impossible to find work. His solicitor claimed that this is the reason why he chose to enrol in the two science courses.
Derek Bell, chief executive of the Association of Science Education, was puzzled by the decision.
"If you have a basic knowledge of things that cause explosions, it wouldn't take that long to piece together how to build a bomb," he said. "But you don't need to do an AS-level chemistry course to get that information.
"I'm sure you could find instructions on the internet."
Mr Bell added that any would-be terrorists could easily find the information contained in an AS-level course, even without attending classes.
"The information in AS courses is open and accessible to everybody," he said. "That's the whole point of education."
Richard Ashley, head of science at Royston High in Barnsley, South Yorkshire, said the ingredients necessary for making explosives are often easy to obtain.
"Boys are always asking us to make fireworks for them," he said. "Anything that goes pop or bang. If they could make their own, they would."
But he also points out that terrorists do not need access to dangerous chemicals in order to cause trouble. They could drive a car into a building or douse a train seat in petrol and set fire to it.
"If a person is intent on causing an act of terrorism, you don't need a qualification," he said.
"The information you need is readily available. Of course, science teachers have the knowledge. But we don't teach it."