Results are reported from experiments in which the high power HF facility at Tromsø, Norway was employed to modify the Hall current region of the auroral ionosphere during periods when the electrojet became enhanced. During conditions characterised by a weak electrojet and completely underdense heating, observations indicated that RF heating leads to the expected increase in the electron temperature, inferred from EISCAT UHF radar measurements, at all altitudes between 100 and 135 km. However, under conditions characterised by a strong electrojet and slightly underdense heating, observations indicated that RF heating appeared to reduce the electrojet electron temperature, in the altitude range 100–115 km, whilst still enhancing the electron temperatures in the layers above the electrojet, in the altitude range 120–135 km. These, somewhat surprising, results are discussed in terms of a theory of the interaction between high power electromagnetic waves and irregularities excited by the Farley-Buneman instability at electrojet altitudes.