Reply To: Flags worn by RN dockyard vessels?
From the 1690s, support vessels employed in HM Service were entitled to wear a Red Ensign, defaced with the relevant seal of the Office concerned.
I would suggest that for the harbour craft, then perhaps the Navy Board flag ? Red Ensign with 3 anchors
see: : https://www.crwflags.com/fotw/images/g/gb_nmm58.gif
The Ordnance Board were responsible for guns and ammo, flag – red ensign with 3 guns and 3 cannonballs
The Victualling Board (food, beer etc) – two anchors in saltire
From 1864 the Red Ensign was changed to Blue