Whether or not there was a formal prohibition, it seems likely that singing during work would be contrary to the Royal Navy's customs and practice, as it would be considered prejudicial to good discipline. It would not have to be spelled out in the Kings Regulations, it might simply be not the "done thing" and therefore not allowed. Especially as in the merchant marine shanties were often used as an opportunity to criticise the officers, which would not be tolerated in the Navy. A tune on a fiddle would be sufficient to co-ordinate effort without allowing the sailors to voice their discontent.

That would not mean shanties might not be used on isolated occasions. A good officer would know when bending the rules and allowing the men to let off steam during a particularly difficult task could prevent future trouble.