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It is important to remove large environmental noise in measurement using SQUIDs without magnetic shielding. Here, the environmental noise has been reduced by an active noise control (ANC) system in the MHz radio-frequency region. The ANC system including a phase and amplitude control circuit has been designed to allow precise adjustments of the phase and the amplitude of the anti-phase wave against the noise waves in the MHz region. In this paper, a sinusoidal wave in the MHz range was used as the radio frequency interference. When a SQUID was used for a signal detector, the ANC system suppressed this sinusoidal wave to the white noise level by about 54 dB. The performance of the ANC system for the chemical detection by nuclear quadrupole resonance (NQR) was checked in a simulated environment. One was the case of a real AM radio broadcasting signal with the dummy NQR signal and another was the real NQR signal with a sinusoidal wave as noise. For both cases, the ANC showed good performance for MHz range noise cancellation.