 -- More than 100 Delta passengers on board a flight bound for Rapid City, South Dakota got an unexpected surprise Thursday night when their plane mistakenly landed at an Air Force Base, about five miles north of the aircraft's intended target.

Ellsworth Air Force Base confirmed in a statement to ABC that while it was an unauthorized landing, "Base officials followed the proper procedures to address the situation and ensure the safety of our Airmen, their families and the passengers."

Both the Federal Aviation Administration and the National Transportation Safety Board are investigating the incident.

"The pilots of the Airbus A320 had been cleared to land at Rapid City Regional Airport. The aircraft instead touched down at Ellsworth Air Force Base, shortly before 7:45 p.m. local time," the FAA released in a statement to ABC News.

Col. Gentry Boswell, 28th Bomb Wing commander at Ellsworth Air Force Base, told ABC News that while the Ellsworth Radar Approach control does control the high-level airspace for approximately 40 miles from the base, the Air Traffic Control Towers at each runway control all aircraft in their local area which is a 5-mile radius up to and including 5,900 feet.

"The Radar Approach Control gave instructions to the Delta flight in this instance and pointed out BOTH runways to the flight crew to alleviate any issues with identification of the correct airport and the crew replied they had the landing runway at Rapid City Regional Airport in sight," said Boswell.

"This was a gross breach of the security of our Airfield that present[ed] a potential threat to both our Airmen and our resources," Boswell added.

According to Boswell, the two runways are located 5 miles from each other and are oriented in roughly the same direction. However, the runway at Ellsworth is 13,500 feet long and 300 feet wide and marked at the threshold with a large "13" number, while the runway at Rapid City Regional Airport is only 8,701 feet long and only 150 feet wide and marked with a large "14."

"Incidents like this occur when pilots fail to execute the basic measures of airmanship," said Boswell.

The flight crew of the Airbus A320 has since been taken off-duty, according to Delta.

"Delta will fully cooperate with that investigation and has already begun an internal review of its own. Safety is always Delta’s top priority," the airline said in a statement.

The flight, which took off from Minneapolis/St. Paul, did eventually leave for Rapid City after coordinating with officials, Delta added in the statement. Expected to land at 8:50 p.m. local time, Delta flight 2845 eventually landed nearly three hours later at 11:31 p.m. local time.

Rapid City Regional Airport Public Information Officer Toni Broom told ABC News "It’s an airline issue and it’s being handled by Delta."

According to the FAA, this is not the first time this has happened. In 2004, a Northwest Airlines flight, also headed to Rapid City, also accidentally landed at Ellsworth Air Force Base.

ABC News Aviation John Nance, a former Air Force Pilot and commercial airline pilot, says this type of incident usually occurs because of "target fixation," when one pilot fixates on an airfield or runway, and neither co-pilot confirms this with the aircraft's navigation aids.

According to Nance, there's usually a distracting element too -- either an issue with the Air Traffic Control Tower, weather, etc.

"The only way you beat it is by specifically training [pilots] so that no one makes a landing without both crew members confirming with the navigational equipment," said Nance.

ABC News' Thomas Thornton contributed to this report.