POLICE are searching for several rifles and shotguns stolen from a Brisbane Catholic school's gun club.

A man and a woman are in custody after one of the weapons was found in the boot of a car, however the rest of the guns are still missing.

Police say about ten weapons and a large amount of ammunition were stolen from a student gun club during a break-in at St Joseph's Nudgee College on Sunday night.

Officers pulled over a car not long after and found one of the shotguns and most of the ammunition in the boot.

Driver Cristle Ten-Bohmer, 27, and passenger Jason Francis Williams, 43, have been charged with weapons and property offences.

Ten-Bohmer wouldn't consent to a police interview but tearfully protested her innocence during a bail application in the Brisbane Magistrates Court.

"I didn't even know that the stuff was in my car," she sobbed from the dock.

"He (Williams) just rang me up and asked me to drive him."

Ten-Bohmer had only met Williams a couple of times, according to duty lawyer Rosemary Gilbert.

Police prosecutor Senior Sergeant Mark Gorton said police were concerned about the outstanding weapons, which were taken from a bunker that was supposed to be secure.

"The worrying thing is, if ten guns went missing and we've only found one, there's nine guns on the street," he told the court.

Magistrate Christine Roney agreed it was concerning and denied Ten-Bohmer bail.

She noted the prisoner's "substantial" five-page criminal history - which contains mostly drug offences - and declared her an unacceptable risk of reoffending.

Williams is expected to appear in the same court on Tuesday.

Originally published as Qld school's stolen guns still missing