In the novel The Clocks, Colonel Beck is the superior of the counter-espionage agent Colin Lamb. Beck's exact department is not stated specifically but it may not be Special Branch. For one thing, neither Beck not Lamb seem to have or use a police rank. Lamb himself tells people that he is not from the police but from a different department. At the end of the novel, Lamb waits for officers from Special Branch to effect an arrest rather than making the arrest himself. Beck's office is not in Metropolitan Police headquarters (where one might expect Special Branch to be located), but up a rickety back staircase of a dingy old bookstore off a sidestreet near to the British museum. While supervising Colin Lamb on the Larkin case, he sends Lamb to Rumania to meet up with a contact to learn as much as he can about someone. Again, that kind of mission would seem unusual for Special Branch.
Beck is assisted by an efficient secretary (a Miss Moneypenny type of character) who is nicknamed "Nanny" by his agents.