Yes, but only in exceptional circumstances and where it is lawful to do so.
The exceptional circumstances for which this policy applies are defined in Interim Guidance to UK Flagged Shipping on the Use of Armed Guards to Defend Against the Threat of Piracy in Exceptional Circumstances (Version 1. 1, published by the DfT in Nov 2011, updated Jun 2012) as: (1) when the ship is transiting the high seas throughout the High Risk Area (HRA); and (2) the latest BMP is being followed fully but, on its own, is not deemed by the shipping company and the ship’s master as sufficient to protect against acts of piracy; and (3) the use of armed guards is assessed to reduce the risk to the lives and wellbeing of those on-board the ship.