SQUID control apparatus for controlling multiple SQUID probes (102) includes a plurality of head units (104) each corresponding to a respective SQUID probe, each of the head units including a non-cryogenic modulated flux-locked loop feedback circuit operating at a respective modulation frequency. The apparatus also includes a base unit (112) coupled to all of the head units, the base unit providing control signals to control the multiple head units. Means are also provided, such as through the use of a daisy chain topology, for synchronizing the modulation frequency of all of the modulated flux-locked loop feedback circuits. The head units may also contain a phase shifter coupled to phase shift the modulation frequency oscillator signal for provision to the local oscillator input of a demodulator, and the phase shifter may include a shifting filter for filtering the oscillator signal to reduce all frequency components except a fundamental frequency component by a desired amount, and shaping means for shaping the filtered and shifted signal into a square wave.