The unnamed policeman was held after other royalty protection officers reported finding ammunition in their personal lockers and bags in a police building in the central London palace's grounds.
"The arrested officer is being questioned on suspicion of misconduct in public office and unlawful possession of ammunition," Scotland Yard police headquarters said in a statement.
"He is in custody at a London police station and will be suspended from duty."
The officer is part of a unit which guards the royal family but was not assigned to protecting any particular figure. Scotland Yard declined to give further details about the nature of the allegations against him.
Four officers from the unit lost their jobs over leaking details of a clash between Andrew Mitchell, then a senior member of Prime Minister David Cameron's government, and police over their refusal to let him ride his bicycle through a gate at Downing Street in 2012.
One of the four was jailed for lying about the incident.