Electromagnetic field (EMF) measurements have limited accuracy, which is additionally impaired by meter self-noise influence. In this paper a novel noise cancellation method is proposed, based on the Hidden Markov Model (HMM) methodology. It allows to calculate the overall field intensity with a much higher accuracy than that obtained from other popular approaches, especially when EMF measurements are close to the noise level. The effectiveness of the new method is illustrated on two EMF datasets, one recorded in an urban and another in a rural area. Its performance is further evaluated in a thorough simulation study using datasets representing the two distinct noisy environments.