George Clooney won best actor for "The Descendants," while Tilda Swinton took the best actress prize for "We Need to Talk About Kevin," in which she plays a grieving mother struggling in the aftermath of her teenage son's school shooting spree.
" 'Hugo' is such a personal film by Martin Scorsese," said Annie Schulhof, NBR president in a statement. "It is a tribute to the early years of cinema that uses today's cutting edge technology to bring the audience into a completely unique and magical world," she said.
The somewhat surprising choice boosted the fortunes for "Hugo," the story of a boy living in a Paris train station who maintains the station's clocks, in the run-up to the Oscars, the film world's highest honors.
The group praised the film, which is based on the book "The Invention of Hugo Cabret" and won strong reviews, as "visually stunning and emotionally engaging."
Other early film awards announced in recent days have focused on a handful of movies including "The Artist," "The Descendants" and "Beginners."
Christopher Plummer won best supporting actor from the National Board of Review for his role as an elderly man coming out of the closet in "Beginners," while Shailene Woodley took the best supporting actress honor for "The Descendants," the story of a man trying to connect with his daughters while his wife is comatose following an accident.
The National Board of Review, a U.S.-based group of movie industry watchers and film professionals, gave its original screenplay award to Will Reiser for cancer comedy "50/50."
Alexander Payne won for adapted screenplay, along with Nat Faxon and Jim Rash, for "The Descendants."
The National Board of Review gave its best animated feature prize to "Rango," while "The Help" was named best ensemble.
The group was formed more than 100 years ago as a nonprofit organization dedicated to supporting movies as an art form and entertainment.
Each year the board also issues a list of top 10 movies, which this year included "The Artist," a black-and-white silent film about the advent of the talkies in Hollywood, and two other presumed Oscar contenders, director Terrence Malick's mystical period piece "The Tree of Life," which stars Brad Pitt, and "The Descendants."
Steven Spielberg's World War I drama "War Horse," Clint Eastwood's film about FBI director J. Edgar Hoover, "J. Edgar," and the Ryan Gosling thriller "Drive" also made the top 10.
"The Girl With the Dragon Tattoo," a remake of the hit Swedish crime film, "Harry Potter and the Deathly Hallows Part 2" and "The Ides of March" rounded out the list.
Absent from the list were some films that have been touted ahead of awards season, including "Take Shelter" and Lars von Trier's "Melancholia."
In other key categories, the National Board of Review gave its best documentary award to "Paradise Lost 3: Purgatory," and chose the Iranian film "A Separation" as best foreign language film.
English actress Felicity Jones was given the award for breakthrough performance for "Like Crazy," as was Rooney Mara for "The Girl With the Dragon Tattoo."
J.C. Chandler received the award for best debut director for "Margin Call" while "Pariah" and "Crime After Crime" were both honored with the Freedom of Expression award.
The Harry Potter franchise was cited for special achievement in filmmaking for the transition from book to film, while actor Michael Fassbender received the spotlight award for several films including "Shame" and "A Dangerous Method."