Heliotron E is a high-shear, large-rotational-transform helical system (ℓ = 2) with 19 field periods and an aspect ratio of 11 (R = 2.2 m, a = 0.2 m). Neutral beam injection of up to 1.7 MW beam power into low-Ohmic-current Heliotron E plasmas has produced plasmas with e ≈ 2.1 × 1013 cm−3, Ti(0) ≈ 0.95 keV, Te(0) ≈ 0.70 keV and β(0) ≈ 1.0%, at a helical magnetic field on the magnetic axis of 1.8 T. This paper describes the ion and electron energy balance for these plasmas, paying special attention to the evaluation of the energy transport coefficients during injection. For the two modes of co-injection and co-injection plus perpendicular injection, the experimental ion and electron thermal diffusivities, χi and χe, are examined using numerical ion and electron temperature profile analysis codes which employ, respectively, the neoclassical ion thermal conductivity and the INTOR-scaling electron thermal conductivity as the reference conductivities. From the measured and calculated ion temperature profiles, it is found that ion heating during injection can be reasonably explained in terms of classical beam power deposition (calculated with a Monte-Carlo beam-orbit code) and the usual neoclassical (Hazeltine-Hinton) thermal conduction processes. An attempt to determine the general behaviour of χe has also revealed that the calculated upper limit of χe during injection is of the same order or less than the INTOR-scaling value.