In 1999 another round of regulations came to force safety and efficiency standards for kei-class vehicles in Japan. Daihatsu met the challenge and received class-leading safety standards for the Hijet Truck. Fuel efficiency and power were also increased with the introduction of the new “TOPAZ” engine, which allowed the Hijet Cargo van to be classified as a low-emissions vehicle in 2002. Additional variants included trucks and vans that ran on LPG and CNG, a hybrid van, as well as an updated EV van model. By 2002 the engine was updated again to include variable valve timing and a turbo option for van models. Variable Valve Timing engines raised output to a max of 53 ps (52.3 hp). Turbo engined vans had increased torque output to 5.6kg-m (76 lb-ft).

The truck model name was officially changed to “Hijet Truck” in 1999 to mark the new model change. Truck models became longer and wider than the previous generation. In 2000 Daihatsu added some additional sales packages, including an anti-rust package with coating backed by a 5 year rust warranty. Power steering became standard equipment from 2003, and air-conditioning was expanded to more trim levels.

From 1999 the commercially focused van was officially called the “Hijet Cargo” and then the Atrai was based on this but more passenger/family focused. Van models featured updated styling from famous Italian designer Giorgetto Giugiaro. Van models had various shapes and grades available, including the deck-van with an open rear cargo area, and “wellcab” version that could easily load wheelchairs for more accessible transport options.