The corroborated sightings were documented in a detailed RAF investigation in files released last week by the Ministry of Defence.
Police officers in Boston and Skegness saw the UFOs above the North Sea on October 5 1996 and contacted the coastguards who in turn alerted ships in the area.
The lights were also observed by the crew of a ship in The Wash and simultaneously air defence radars at RAF Neatishead in Norfolk detected an unidentified blip over Boston.
But the RAF report concluded that the radar imagery was caused by Boston Stump's spire.
It read: "The church spire is known in aviation circles as the Boston Stump and appears occasionally on some radars in certain radar propagation conditions."
But the lights in The Wash area were harder to explain and were suggested to be "a distant celestial source".
The report read: "The lights in The Wash area were observed from three separate locations high above the horizon and in the same general direction, but without corroborating radar data.
"No associated air vehicle was detected by civil or military radars. This suggests a distant celestial source.
"There were no corroborating radar returns for the visual sightings."