The operation targeting the bookstore was launched on Wednesday morning at Logan, the ABC reported.
The AFP confirmed to AAP that there was a raid.
"The AFP/QPS (Queensland Police Service) can confirm it is conducting operational activity in Brisbane this morning," it said in a statement.
"As this is an ongoing operation, no further comment can be provided at this stage."
AFP said the raid was occurring in the Logan suburb of Underwood.
The AFP has not identified the specific property targeted in the raid.
But pictures have emerged on line showing officers outside the iQraa Islamic Centre in Underwood.
A key figure at the bookshop, who's mentioned in a promotional video, is Omar Succarieh.
Last week, The Courier-Mail reported a man, believed to be the brother of Australia's first suicide bomber in Syria, was running an Underwood bookshop.
A centre Facebook post on September 6 rejected reports it was promoting extremism.
"Islam and this centre does NOT tolerate extremism but not what the disbelievers portray extremism is," the post read.
"We do not discriminate either, so we have allowed many speakers to come and give lectures and share their views here."
AAP sought comment from the centre on Wednesday but the phone rang out.
The iQraa Islamic Centre is believed to have hosted a lecture this year on what followers should do if they were contacted by ASIO.
Outgoing ASIO chief David Irvine on Tuesday said the spy organisation was actively considered raising Australia's terror threat level, from medium to high.
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