The building, designed by Reiach and Hall and home to the national archive for the civil nuclear industry, won Public Building of the Year and the Editor's Choice of the Year awards.
The prestigious awards celebrate design excellence in UK architecture across 23 different categories at an event held in London.
Morrison Construction Managing Director for the Highland business Donald Mclachlan said: ''We are delighted at the recognition this wonderful facility has achieved on a national stage.
''Our highly-skilled teams work extremely hard to deliver excellent facilities to benefit the communities they are built in many years into the future.''
Architects' Journal Architecture Awards judges commented: "This is an exceptional piece of architecture materially, aesthetically and functionally: it's made well, looks stunning and fulfils, indeed exceeds, its brief – effectively reimagining what an archive building can be in both form and function."
Nucleus facility was opened earlier this year and includes a large public area, reading room and community space.
More than 70 years' worth of information and up to 30 million digital records are held in the facility, which also contains local archives dating back to the 16th century.