The civilian lorry was stopped at gate eight of the RAF base at around 8.50am after a military working dog alerted security staff.
Police have put a 1km cordon around the base and partly closed the A1065.
As a precautionary measure, gate eight, which is usually used by HGV vehicles, was closed and MoD responded by diverting traffic from the A1065 along the stretch from the B1112 to Wangford Road.
Suffolk Police were called at 9.25am and were still in place this afternoon.
Base officials have also closed the main gate for the base, gate one.
