Security staff and police were called while the jury were taken out of their room.
The door was taken off its hinges before the intruder was removed out a back entrance.
A Child, Youth and Family spokeswoman said they were looking into the incident, along with the Ministry of Justice.
"We continue to work with the young woman and support her through some challenges she is facing."
The kidnapping and assault trial of Kaiapoi businessman Dave Clemence, was delayed for about 10 minutes while the woman was removed.
Judge Gary MacAskill apologised to the jury when he finally got on the bench and began his summing up.