Scotland Yard says personal beliefs must not be put above police duties, after a constable refused to shake hands with Sir Ian Blair.
Sir Ian "questioned the validity of the request", Scotland Yard said
The Muslim woman officer refused to shake hands with the Metropolitan police chief on religious grounds.
It happened when Sir Ian inspected 200 recruits at a passing out parade.
The Met says the officer puts the job's requirements above her personal beliefs, which she only exercises where there is a choice.
"Any refusal to engage in this manner would not be tolerated by the Metropolitan Police Service," it added.
It said the officer's request not to shake her boss's hand was only granted "out of a desire to minimise any disruption to others' enjoyment, and to ensure the smooth running of what is one of the most important events in an officer's career."
The commissioner questioned the validity of the request, and the matter is being looked into by the MPS, it said, adding that an officer's probationary period is designed specifically to ensure that "they undertake the role as required".
If this does not occur the officer may be required to leave the Service as any variation on this will not be tolerated.
The woman had said it was contrary to her religious teaching to touch a man, the Mail on Sunday reported.
The woman, who wore a uniform hijab, also refused to be pictured with Sir Ian at the event on 21 December as she did not want a photo used for "propaganda purposes", the paper said.
The incident took place at Imber Court, the Metropolitan Police Service's sports and conference centre at Thames Ditton, south-west London.
The Mail on Sunday said the Pc, described as a "non Asian Muslim", was among recruits who had competed 18 weeks of basic training.
Several Muslim groups have defended the officer's actions and insisted it would not affect how she carried out her job.
Massoud Shadjareh, chairman of the Islamic Human Rights Commission, said the "overwhelming majority" of practising Muslims would avoid physical contact with members of the opposite sex.
"Muslims do not physically touch members of the opposite sex unless they are married or very closely related - for example, brother and sister or uncle and niece," he said.
"This is not a sign of disrespect or anything."
He added that those employed in jobs such as police officers or doctors would not have a problem with touching people in order to fulfil their duties.
"I actually think the only problem is when there is cultural and religious ignorance and misunderstanding," he said.