The objectives of the JET Neutral Beam Enhancement (NBE) include raising the delivered power from the present 25MW to >34MW and increasing the pulse length from 10s to 20s. The additional power will be obtained partly by increasing the fractional energy components of the beam, resulting from acceleration of molecular ions, hence increasing the total particle flux. These changes place extreme demands on the design of the upgraded protection to the torus entry duct. The present inertial duct protection already reaches its thermomechanical limit in 10s pulses, and active cooling of the upgraded duct protection is therefore essential. Extensive analysis of the pressure and temperature evolution in the present un-cooled duct established the relationship between gas re-emission and surface temperature for copper in this operating environment. This information was used in an integrated physics and engineering approach to the design of the actively cooled duct protection, taking into account the power loads from direct beam interception and re-ionisation. Surface temperature determines power density through the gas re-emission and consequential beam reionisation. These considerations define the normal operating point for the chosen enhanced hypervapotron element technology. This approach demonstrated that supplementary in-situ duct cryopumping would not be needed, provided that the required heat-transfer performance could be met without any encroachment of the elements beyond the space envelope of the existing inertial duct protection plates. This requirement posed severe constraints on the mechanical design of the hypervapotron element array and its manifolding; the adopted engineering design solutions are presented.