Pentagon officials said in a statement that the security officers´ wounds did not appear to be life-threatening.
They added that the suspect was in custody but his condition was not known.
All entrances to the five-sided headquarters of the U-S Defense Department in Virginia were closed soon after the shooting at 6:40 p-m local time.
All entrances were later reopened, except the one adjacent to the Metro station.
Officials said an investigation was just starting.
It was unclear why the alleged gunman opened fire at the Pentagon security officers.
Some witnesses reported hearing gunshots being fired in the Metro station and people screaming.