Army Col Steve Warren said the increase was not the result of a specific event.
He said it was the result of an increased threat climate, including the arrests of several suspected Islamic State sympathizers in the US.
The increase likely means more bag and vehicle checks at military facilities.
The military has four levels of security that are labelled A through D.
The decision moves the baseline level from A to B at all facilities, even though most were already engaging in stricter security measures individually.
It comes several days after two men tried to attack a conference in Texas which included a contest to draw cartoons of the Prophet Mohammed; they were shot dead by police.
The US military has increased its threat level at facilities across North America, although most installations were already operating at a higher level of protection.