Hours after The New York Times published an article on Thursday that examined deep flaws in the N.F.L.’s early concussion research and the league’s ties to the tobacco industry, the league responded with a statement disputing various aspects of the article.

The statement said the article was “contradicted by clear facts” and that The Times “published pages of innuendo and speculation.”

Data obtained by The Times revealed that more than 100 diagnosed concussions were not included in the studies that formed the backbone of the league’s early stance on the issue. The research was held up by the league as evidence that brain injuries did not cause long-term problems for players.

■ The N.F.L. statement said, “The Times claims that the concussion studies funded in part by N.F.L. Charities purposely relied on faulty and incomplete concussion data.” Our article did not claim that.