Ringa Atawhai has had the office at the Whangarei Terenga Paraoa for six months, offering community health services.
The man apparently entered the building by opening the window and climbing in.
A member of the public who saw what happened called 111, Mr Weston said. Whangarei police arrived at the scene and found the teen using the toilet in the building.
When he tried to run from the police he bowled down a door between the Ringa Atawhai building and wharekai.
A man was arrested and charged with burglary.
Ringa Atawhai manager Ces Smith said she was saddened by what had happened.
"I got the call from the police and went straight down to the office. I was saddened and very disappointed to hear it was one of our own who had violated our space like that," she said.
"In our 30 years we have never been broken into. The marae has never been broken into either. It's sad to think he would choose that one sacred place to violate," she said.
She said the fact the man had used the toilet was awful.
"He must have been high or drunk or something, and he was probably full of anger," she said.
Ms Smith said the doorway and window will have to be replaced, but they are grateful to not have lost any valuables.
She said she would consider the possibility of restorative justice, but only if the man's whole family would be involved in the process.
Mr Weston said police were thankful for the member of the community who called 111 so the police could get to the scene and arrest the suspect.
He was taken to the station and was due in court yesterday.
