These sets are classified E2', and are equipped with retractable nose-end couplers at the Morioka end.

A further four J sets were delivered in October/November 1998 to augment the fleet to coincide with the introduction E2 series stock on four return Asahi services between Tokyo and Niigata on the Jōetsu Shinkansen from the start of the revised timetable in December 1998.

The last remaining original "J" sets were withdrawn before the start of the revised timetable on 16 March 2019.

[1] The prototype E2-1000 series train (unit J51) was delivered as an 8-car to Sendai depot in late December 2000, and entered revenue-earning service in November 2001 after extensive testing.

Unlike the earlier J sets, these units are only compatible with the 50 Hz power supply of the Tohoku and Joetsu Shinkansen routes and they aren't equipped with slope-usable brake systems.

While J51 was delivered in the same livery as earlier E2 series trains, units J52 onward were delivered from new in the Hayate livery with a magenta waistline stripe in place of the previous red and a new "apple" logo in place of the "wind" logo on the original batch of J and N units.

Seating is 2+3 in standard class with a seat pitch of 960 mm (38 in), and 2+2 in green class with a seat pitch of 1,160 mm (46 in).An E2-1000 series train (J56) broke the Japanese rail speed record for a production train (i.e. not a dedicated test train) in April 2003 when it reached a speed of 362 km/h (225 mph) during a series of late-night high-speed test runs between Urasa and Niigata on the Joetsu Shinkansen.

[11][failed verification] To celebrate 150 years of rail transport in Japan, JR East announced plans in 2022 to repaint a set into a livery similar to that of the 200 series when they first entered service in 1982.

Set J69 with the special wrap, nicknamed the Magical Dream Shinkansen, was introduced on 22 December 2023.

Car E223-23[16] of former set J10 was moved from Sendai Depot to Sanwa Tekki Corporation in Utsunomiya, Tochigi, in February 2017, where it is preserved.

Car E224-127 of former set J14 was moved from Sendai Depot to the Hirosawa City theme park in Chikusei, Ibaraki, in November 2018, where it is preserved.