A sterilisation tunnel of pharmaceutical containers, comprising: an inlet opening, for inlet of containers to be sterilised, an outlet opening, for outlet of the sterilised containers; at least a sterilisation chamber, for sterilisation of the containers at high temperature, and a cooling chamber, for cooling the sterilised containers, consecutive to the sterilisation chamber and communicating with the outlet opening; a conveyor means, for receiving the containers from the inlet opening and for transporting the containers through the sterilisation chamber and the cooling chamber up to in proximity of the outlet opening; a transfer plane, situated consecutive to the conveyor means, wherein the transfer plane is mounted with respect to the conveyor means so as to be arrangeable in a first alignment configuration, wherein it is aligned to the conveyor means and arranged at the outlet opening, in order to receive the sterilised containers from the conveyor means and enable transfer thereof externally of the tunnel through the outlet opening; a shutter, arranged and movable with respect to the outlet opening and with respect to the transfer plane so as to be positionable in a raised position, in order to maintain the outlet opening open and enable outlet of the sterilised containers, and in a first lowered position, abutting the transfer plane, in order to close the outlet opening; characterised in that the transfer plane is mounted with respect to the conveyor means in such a way as to be movable and positionable in a second misaligned configuration with respect to the conveyor means wherein the transfer plane is misaligned with respect to the conveyor means and arranged internally of the cooling chamber of the tunnel, and in that the shutter, when the transfer plane is moved and positioned in the second misaligned configuration and arranged internally of the cooling chamber, is movable in order to be positioned in a second lowered position, at a lower height than the first lowered position, in which the shutter is positioned abutting a seal element. an inlet opening, for inlet of containers to be sterilised, an outlet opening, for outlet of the sterilised containers; at least a sterilisation chamber, for sterilisation of the containers at high temperature, and a cooling chamber, for cooling the sterilised containers, consecutive to the sterilisation chamber and communicating with the outlet opening; a conveyor means, for receiving the containers from the inlet opening and for transporting the containers through the sterilisation chamber and the cooling chamber up to in proximity of the outlet opening; a transfer plane, situated consecutive to the conveyor means, wherein the transfer plane is mounted with respect to the conveyor means so as to be arrangeable in a first alignment configuration, wherein it is aligned to the conveyor means and arranged at the outlet opening, in order to receive the sterilised containers from the conveyor means and enable transfer thereof externally of the tunnel through the outlet opening; a shutter, arranged and movable with respect to the outlet opening and with respect to the transfer plane so as to be positionable in a raised position, in order to maintain the outlet opening open and enable outlet of the sterilised containers, and in a first lowered position, abutting the transfer plane, in order to close the outlet opening; characterised in that the transfer plane is mounted with respect to the conveyor means in such a way as to be movable and positionable in a second misaligned configuration with respect to the conveyor means wherein the transfer plane is misaligned with respect to the conveyor means and arranged internally of the cooling chamber of the tunnel, and in that the shutter, when the transfer plane is moved and positioned in the second misaligned configuration and arranged internally of the cooling chamber, is movable in order to be positioned in a second lowered position, at a lower height than the first lowered position, in which the shutter is positioned abutting a seal element.