Methanol and water vapour masers are signposts of early stages of high-mass star formation but it is generally thought that due to different excitation processes they probe distinct parts of stellar environments. Here we present observations of the intermediate-mass young stellar object G107.298+5.639, revealing for the first time that 34.4 d flares of the 6.7 GHz methanol maser emission alternate with flares of individual features of the 22 GHz water maser. High angular resolution data reveal that a few components of both maser species showing periodic behaviour coincide in position and velocity and all the periodic water maser components appear in the methanol maser region of size of 360 au. The maser flares could be caused by variations in the infrared radiation field induced by cyclic accretion instabilities in a circumstellar or protobinary disc. The observations do not support either the stellar pulsations or the seed photon flux variations as the underlying mechanisms of the periodicity in the source.
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