An intruder alert was an alert aboard a starship that reported the presence of someone who was not supposed to be aboard ship.
In 2275, efficiency auditor Aaron Kelly sounded the intruder alert aboard the USS Enterprise in order to test the efficiency of security's response. Security chief Pavel Chekov responded quickly and ended up punching Kelly in the face. He then took Kelly into custody for violating starship regulations. (TOS novel: Death Count)