Metropolitan Police Commissioner Sir Bernard Hogan-Howe made his comments as 11 women and one man, who claim to have been deceived into having such relationships, take legal action against forces.
Former Scotland Yard officer Bob Lambert, a terrorism expert at the University of St Andrews, earlier this year apologised to the women he had relationships with while undertaking the work.
Sir Bernard said yesterday the force had guidelines that say police moles should not get involved in sexual relationships, but that the rules could not prevent "human beings failing".
However this was dismissed by one of the lawyers representing the group as "ridiculous".
Sir Bernard told the London Assembly Police and Crime Committee: "We have a policy that says that our officers should not engage in sexual activity with targets or anyone else they meet, or a victim, while they are serving as a police officer. Any policy cannot prevent human beings sometimes failing. What we need to know is, if that should happen and an individual does have sexual activity, that their manager knows and will react to that."