The original Atkinson cycle engine used a complex system of pushrods and gears to make the compression/power strokes shorter than the intake/expansion strokes. The Prius uses variable valve timing and computer controls to achieve the same end. So it depends on your definition of "true". If you only consider that engines with a complex system of pushrods and gears to be "true" then it doesn't. If it's the end result that matters then yes, it's a "true" Atkinson cycle engine. An Atkinson cycle engine differs from a Miller cycle engine in that the Miller cycle engine always uses some device to push air into the system (super charger or turbo charger) while the Atkinson cycle engine is naturally aspirated.
Check out this site for a more detailed look at how the Prius works:
http://www.ecrostech.com/prius/original/PriusFrames.htm
Although this site only covers the 2001-2003 Prius, the basic principles are the same, only the implementation details vary.
www.ecrostech.com