Secret court hearings - known as closed material procedures - are part of the TPim process.
It is believed to be the first alleged breach of the Terrorism Prevention and Investigation Measures (TPim).
The defendant was granted unconditional bail although he remains subject to the restrictions imposed by his TPim.
Ten people in the UK are currently subject to a TPim notice, according to the Home Office.
The court heard that BM is charged with two counts of breaching Section 23 of a TPim order.
The BBC is not aware of anyone else who has appeared in court charged with a breach of a TPim.
Those subject to a TPim can be ordered to stay overnight at a specified address and report to a police station every day.
Ministers say they do not believe his disappearance is linked to any terrorism planning in the UK, and his TPim was intended to prevent fundraising and overseas travel.
The suspect - who can only be referred to as BM - was one of nine British citizens subject to a TPim when the figures were last disclosed in March.
There is a higher threshold for the imposition of a TPIM (reasonable belief that the individual is or has been involved in terrorism-related activity) than existed with control orders (reasonable suspicion of involvement in such activity).
Ms Cooper also asked whether preparations were in place for a Terrorism Prevention and Investigation Measures (TPim) - but warned it would be weaker than the control order created by Labour but scrapped by the coalition.
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