Civilians acting as unofficial guards have appeared outside some centers since five service personnel were shot dead last week in Chattanooga, Tennessee.
Military personnel are generally barred from carrying firearms at recruitment centers and bases.
The Pentagon says it appreciates the support but armed civilians could pose an unintended security risk.
In a statement spokesman Peter Cook said: “While we greatly appreciate the outpouring of support for our recruiters from the American public, we ask that individuals not stand guard at recruiting offices as it could adversely impact our mission, and potentially create unintended security risks.
“We continue to partner with and rely on first responders for the safety of the communities where our service members live and work.”
According to officials, the Chattanooga gunman – 24-year-old gunman Muhammed Youssef Abdulazeez – acted alone when he attacked two military facilities, killing five service members.
Muhammed Youssef Abdulazeez was shot and killed by police during the attack. His motive was unclear.
Since then, armed civilians – some of them members of private militias – have turned up outside recruitment centers saying they are supporting those inside.
One group appeared in Cleburne, Texas, armed with assault rifles and calling themselves Operation Hero Guard.
In Lancaster, Ohio, armed civilians were ordered off the property after one accidentally discharged his rifle into the pavement.
US officials say there is no indication of further danger to recruitment centers and the government does not intend to change the way they are staffed.
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