Two people were taken into custody after police say they broke into Mission San Juan Thursday evening.
A man and woman were caught breaking into the federal building around 8 p.m.
Park police say the church has been under construction so it was not clear what the suspects were trying to take.
Park police say they will have to wait until daylight Friday to determine exactly how much damage was done.
Police have not said what charges the two may face or released their names.