Other winners announced at London's Tate Modern included American painter Ellsworth Kelly and film and stage composer Stephen Sondheim, who wrote the lyrics to West Side Story.
Lord Rogers, 66, whose acclaimed modernist buildings also include the Pompidou Centre in Paris and the Lloyd's Building in the City of London, scooped one of five Praemium Imperiale Awards worth £90,000.
Other winners announced at London's Tate Modern included American painter Ellsworth Kelly and film and stage composer Stephen Sondheim, who wrote the lyrics to West Side Story.
The Ulster Youth Orchestra was awarded the special additional prize of £30,000 as a Grant for Young Artists.
Lord Rogers and the other prize winners are due to attend a special audience with the Queen on Wednesday before receiving their cash awards at a ceremony in Tokyo in October.
Architectural adviser
The Florence-born Millennium Dome architect is internationally famous for combining modern architectural style and new technology for aesthetic effect.
He joined forces with Renzo Piano to design the Pompidou Centre, and after its completion in 1977 formed his own company, the Richard Rogers Partnership.
Lord Rogers was awarded the Royal Gold Medal for Architecture in 1985 and then knighted in 1991.
He was made a life baron in 1996 and appointed chairman of the Government's Urban Task Force two years later.
He joined the newly formed cabinet of London mayor Ken Livingstone last month as an advisor on architecture and planning.
The Praemium Imperiale Awards, presented annually by the Japanese Arts Association since 1988, recognise lifetime achievement in the fields of painting, sculpture, architecture, music and theatre or film.
They are widely seen as the artistic equivalent of the Nobel Prizes for science.
Past laureates have included the late Sir John Gielgud, actor-director Lord Attenborough, artist David Hockney and sculptor Louise Bourgeois, whose giant spider and towers are currently focal exhibits at Tate Modern.
The full list of Year 2000 winners is: