Following the privatisation of JNR on 1 April 1987, JR Freight received the prototype (EF66 901) and 39 of the original series (EF66 1 to EF66 39) as well as the Class EF66-100 machines.
JR West obtained the remainder of the machines (EF66 40 to EF66 55) - a total of 16.

Shortly after privatization, JR Freight tried out a number of new experimental liveries on its various locomotives, and one Class EF66, locomotive number EF66 20, received an experimental cream and blue livery with large "JR" logos in August 1987.
No other members of the class were reliveried, however, and EF66 20 received the new JR Freight two-tone blue livery when it underwent refurbishment in October 1993.

From 1988, JR Freight retrofitted a number of its EF66s (numbers 22 - 24, 26 - 27, 30 - 33, 37) with roof-mounted cab air-conditioning units.

From 1993, JR Freight started refurbishing its fleet of EF66s (numbers 1 - 5, 7 - 10, 11 - 12, 16 - 39, 41, 44, 53, 55).
Refurbishment included rewinding of the traction motor coils, removal of the former JNR decorations on the front-end number plates, and repainting into a two-tone blue livery similar to that carried by the EF66-100s.
Locomotives refurbished from 2004 onward, however, received a simplified blue livery, similar to the original JNR-style livery.
Following the privatisation of JNR on 1 April 1987, JR Freight received the prototype (EF66 901) and 39 of the original series (EF66 1 to EF66 39) as well as the Class EF66-100 machines. JR West obtained the remainder of the machines (EF66 40 to EF66 55) - a total of 16.
Shortly after privatization, JR Freight tried out a number of new experimental liveries on its various locomotives, and one Class EF66, locomotive number EF66 20, received an experimental cream and blue livery with large "JR" logos in August 1987. No other members of the class were reliveried, however, and EF66 20 received the new JR Freight two-tone blue livery when it underwent refurbishment in October 1993.
From 1988, JR Freight retrofitted a number of its EF66s (numbers 22 - 24, 26 - 27, 30 - 33, 37) with roof-mounted cab air-conditioning units.
From 1993, JR Freight started refurbishing its fleet of EF66s (numbers 1 - 5, 7 - 10, 11 - 12, 16 - 39, 41, 44, 53, 55). Refurbishment included rewinding of the traction motor coils, removal of the former JNR decorations on the front-end number plates, and repainting into a two-tone blue livery similar to that carried by the EF66-100s. Locomotives refurbished from 2004 onward, however, received a simplified blue livery, similar to the original JNR-style livery.
JNR Class EF66