Abstract: A method and apparatus for controlling implantation during vacuum fluctuations along a beam line. Vacuum fluctuations may be detected based on a detected beam current and/or may be compensated for without measuring pressure in an implantation chamber. A reference level for an ion beam current can determined and a difference between the reference value and the measured ion beam current can be used to control parameters of the ion implantation process, such as a wafer scan rate. The difference value can also be scaled to account for two types of charge exchanging collisions that result in a decrease in detected beam current. A first type of collision, a non-line of sight collision, causes a decrease in detected beam current, and also a decrease in the total dose delivered to a semiconductor wafer. A second type of collision, a line of sight collision, causes a decrease in detected beam current, but does not affect a total dose delivered to the wafer.