"Today's New York Times article and headline, written by individuals who have not seen the film, contains many misleading inferences," a studio spokesman said in an e-mailed statement.
"As will become immediately clear to anyone actually seeing the movie, nothing with regard to this important story has been 'softened' to placate anyone."
The movie due for release in December tells the story of Nigerian-born forensic neuropathologist Bennet Omalu, played by Smith, and his diagnosis of chronic traumatic encephalopathy (CTE) in the brains of deceased NFL players who suffered multiple concussions.
Omalu's work was first widely publicized in the 2013 Frontline documentary "League of Denial".
Concussions have become a major injury concern for the league, which agreed to pay $765 million to retired players to settle concussion-related health claims after accusations it long ignored evidence that head injuries posed long-term risks to players.
The New York Times, citing internal Sony emails that were made public in last year's cyberattack on the studio blamed on North Korea, reported that the studio was concerned not to condemn the NFL -- a financial juggernaut that boasts an estimated $10 billion (7.6 billion euros) in annual revenues and a combined value for its 32 teams of $45.76 billion.
The NFL's place as steward of America's most-watched game and it's links to various television networks and corporate sponsors make it an entertainment as well as a sports juggernaut.
However, in addition to Sony's statement on Wednesday, "Concussion" writer and director Peter Landesman told Deadline.com that it seemed to him the New York Times "is working for the NFL".
"It seems like a hatchet job has been done here, and came out of the NFL's offices," he told the entertainment news website.
Although the film is slated for a Christmas release, Sony released a trailer on Monday, and has screened it for some prominent figures in the sports world.
That includes sports broadcaster Bob Costas.
"I have seen the movie," Costas said in a statement issued through Sony.
"As one who has followed, and commented on, this issue, it doesn't appear to me many punches were pulled."