At the same time, Bemidji Aviation Services flight 46 (BMJ46), a Beech 99 cargo flight with only the pilot aboard, was cleared for takeoff on runway 30L en route to La Crosse, Wisconsin. Weather conditions at the time were reported as a 900-foot ceiling and 10 miles visibility below the clouds. Immediately after departure, the tower instructed the US Airways crew to turn left and head west, causing the flight to cross paths with the cargo aircraft approximately one- half mile past the end of runway 30L.

Neither pilot saw the other aircraft because they were in the clouds, although the captain of the US Airways flight reported hearing the Beech 99 pass nearby. Estimates based on recorded radar data indicate that the two aircraft had 50 to 100 feet of vertical separation as they passed each other approximately 1500 feet above the ground.

The US Airways aircraft was equipped with a Traffic Alert and Collision Avoidance System (TCAS) that issued climb instructions to the crew to avert collision. The Beech 99 was not equipped with TCAS and the pilot was unaware of the proximity of the Airbus. There were no reports of damage or injuries as a result of the incident. NTSB and FAA investigators conducted a preliminary investigation at the Minneapolis airport traffic control tower on September 18th and 19th and are continuing to review the circumstances of this incident.

The Beechcraft Model 99 was produced by the Beech Aircraft Corporation (previously the Beechcraft Division of Raytheon and now a unit of Hawker Beechcraft). It is also known as the Beech 99 Airliner and the Commuter 99. The 99 is a twin-engined, unpressurized, 17-seat/15 passenger turboprop aircraft. Is first flight was in July 1966 and production ended in 1986. Nearly half the Beech 99s in service today are now operated as freighters.