The Independent Police Complaints Commission (IPCC) is set to announce on Tuesday that it has asked police to pass on complaints or other queries about the legislation.
IPCC chairman Nick Hardwick told Britain's The Guardian newspaper that representatives from Muslim groups feared their community was being disproportionately targeted by the police.
Muslim groups had already raised "some very significant issues" with the watchdog, he added.
"The police must give the highest priority to protecting the public from the threat of terrorism," Hardwick said.
Lack of confidence
"But there is no doubt that the use of these exceptional powers has undermined confidence in the police.
"It is essential Muslims don't feel unsafe and discriminated against and I hope by calling in these complaints we can provide independent reassurance that special powers are being used in an accountable and proper way."
Police have made a series of arrests under anti-terror laws which were notably toughened up after the 11 September 2001 attacks in the US.
Some Muslim groups complain that police raids have targeted Muslim areas indiscriminately, and that a high proportion of those arrested are soon found to be innocent and freed.