Carlile said there was "ample anecdotal evidence" that people were being stopped to produce a racial balance in the statistics, which he said was an invasion of their civil liberties.
"I can well understand the concerns of the police that they should be free from allegations of prejudice.
"But it is not a good use of precious resources if they waste them on self-evidently unmerited searches," he said.
"The criteria for Section 44 stops should be objectively based, irrespective of racial considerations.
"If an objective basis happens to produce an ethnic imbalance, that may have to be regarded as a proportional consequence of operational policing."
The majority of prisoners (91 percent) convicted of terrorism offences in England and Wales classify themselves as Muslim, while just over half those remanded on terrorism offences are of Asian ethnic origin.
A Home Office spokesman said stop and search helped deter terrorist activity but that maintaining good community relations was also important.
"We are continuing to work with the police to ensure that the use of stop and search powers strikes the right balance," he said.