A disk drive has a servo control system that implements just-in-time (JIT) seeks with low power consumption for all long seeks. The servo controller receives a seek command to move the transducer to a target data track and sector, calculates rotational latency from the seek command, and limits the transducer velocity for seeks longer than a predetermined seek length. The servo controller then generates a JIT gain from the calculated rotational latency, modifies the transducer acceleration and deceleration using the JIT gain, and modifies the transducer velocity limit using the JIT gain. Positive current is applied to the actuator to move the transducer with the JIT gain-modified acceleration until the transducer reaches the modified velocity limit. The servo controller determines when to initiate deceleration of the transducer, and applies negative current to the actuator to move the transducer with the JIT gain-modified deceleration until the transducer reaches the target track.