Phone operators at Scotland Yard's control room will have to make a record of when they nip to the loo.
The Met says the new rules will stop staff at Lambeth's control room from taking unnecessary breaks.
Employees will have to note toilet visits as a "code three" and they will be recorded on a database.
However, staff aren't happy about the change. Employee Paul Drew wrote in a staff magazine: "Everyone I have spoken to about this finds it deeply offensive and humiliating.
"It would be interesting to know what the public or the Met can possibly gain from making notes of such intimate details."
Superintendent Russ Hanson-Coles, told the BBC: "Our primary role at central communications command is to be available for the public to contact and it is vital that we make the best use of our resources.
"Staff in this environment have regular breaks that compare very favourably with outside industry so the need for extra personal breaks should be minimal."
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