Major safety concerns identified for the Muon Arms are (1) Gas flammability (provided, flammable gas mixtures are chosen for physics reasons) (see section 2.10.2), (2) Personnel safety while accessing chambers or electronics in either enclosed spaces like the lampshades or at elevated locations given that half of the octants are above the nominal beam pipe height, and (3) oxygen deficiency hazard when working in enclosed spaces. Issues common to other tracking systems are discussed in Section 2.11.2.

The safety of the Muon Arms would be enhanced if non-flammable gas mixtures are selected and used exclusively. That has turned out to be possible only in the Muon Identifier where a non-flammable mixture of CO₂-Isobutane, 91-9%, is used. The presence of the steel lampshade which encloses the Muon tracking chambers and the muon ID steel provides some isolation of the chambers and proportional tubes from the from the rest of the PHENIX experiment that is not enjoyed by other gas filled chambers used in the detector carriages. This mitigates some of the fire and explosion hazard presented by those detectors, as discussed specifically in the DBA. Analysis presented in Section 2.10.2. For the Muon Tracker there is a fire and explosion hazard similar to that of the tracking chambers and RICH detector and mitigation of this hazard has been outlined in Sections 2.10.2 which discusses flammable gas hazards and mitigation. As extra precautions the Muon ID flows nitrogen into the aluminum panels outside of the tubes. The exit nitrogen will then flow through sensor to detect leaking tubes. If isobutane above an as yet to be determined amount is detected the system will shut down and notify the operator as stated in the fault chart of Section 2.11.2.