The move aims to beef up security at the border areas amid increasing threat of global terror attacks, according to ICA.
The thumbprint scanning system will first be introduced at sea and land checkpoints. Airport checks will follow.
Singapore citizens and residents who use the enhanced Immigration Automated Clearance System (eIACS) or automated clearance lanes for departure and arrival will not be affected by the regulation.
ICA noted that travellers might experience slightly longer immigration clearance times at the checkpoints due to the regulation.