It is the second inquiry to be started after the Herald published stories based on top-secret GCSB and National Security Agency documents. The first inquiry was into New Zealand spying in the Pacific.
Ms Gwyn said the new inquiry was instigated by her office.
"I consider the issues raised about the process followed when the GCSB considers undertaking particular intelligence activity are of sufficient public importance to warrant an own-motion inquiry.
"While it is unlikely I will be able to publicly confirm or deny the specific allegations relating to this process, I can inquire more generally into how the GCSB determines, within its statutory constraints, what intelligence activity to undertake and what policies and procedures are in place to regulate its activities."
Ms Gwyn said the inquiry would study how the GCSB established whether a proposed spying job fitted its legal role and New Zealand's needs.
It would also look at the GCSB analysis of benefits and risks, and how it handled situations in which there could be perceptions of political advantage.
It would also consider how the GCSB kept its minister informed in situations where there was a "potentially contested assessment" of the justification for the spying.
The Herald reported that the GCSB set up search filters to extract online references to those competing from other countries for the WTO job.
Criticism was voiced after the story appeared over how this served New Zealand's interests as the WTO job is meant to be administrative and neutral.