When the New York Times NYT -0.99% published a detailed investigative report on Thursday calling into question the National Football League’s research on concussions, the league responded with a 2,500-word rebuttal.

On Friday the league upped the ante, running ads on the Times’ website, including the very article that caused the firestorm.

The Times’ online sports section, even non-football stories, featured numerous ads from the NFL highlighting the changes the league has taken to improve player safety as a debate rages over the medical effects of concussions.

The banner ads could be seen early Friday across the top of stories, with a larger half-page ad on the right side. (See the screenshots embedded in this article.) By mid-afternoon on Friday, Wall Street Journal reporters could no longer find the ads on the site. A Times spokeswoman said the ads were still in circulation, however.

The NFL took out ads in the New York Times’ investigative story on concussion research. Photo: New York Times

A spokesman for the NFL said the league bought the ads because it wanted to present information directly to readers, rather than have it filtered through the Times’ editorial staff. The league contends that it was transparent about the limitations of the data used in the research the Times cited.

“We wanted readers to have all the information about all the work that we’ve done to improve the safety of the game,” said NFL spokesman Brian McCarthy. “We were concerned that our message was being mishandled by the Times.”

Mr. McCarthy said this was the first time the NFL has purchased display ads to counter such a story. He said the NFL also paid to promote its message on Facebook and Twitter.

In an email, the New York Times spokeswoman declined to comment on whether the ads were sold directly by the Times’ ad sales staff to the league or through a third-party seller.

“We do not discuss the terms of advertising agreements,” she said.

Photo: New York Times

The spokeswoman pointed to the Times’ standards for advocacy ads, which say the paper accepts ads “in which groups or individuals comment on public or controversial issues. We make no judgments on an advertiser’s arguments, factual assertions or conclusions.”

The Times has vigorously defended its reporting, including a point-by-point counter to the NFL’s rebuttal.

The Times’ report alleged that the NFL’s research undercounted the number of player concussions, skewing its studies. The story also reports that there were ties between the league and the tobacco industry, including shared lawyers, lobbyists and consultants. A league lawyer told the Times the NFL had no connection to the tobacco industry.

Patrick Hillmann, senior vice president at Levick, a public relations firm, said the NFL’s strategy of an all-out digital assault in its response is becoming increasingly common for companies and organizations in crisis situations.

“Before you can begin to respond to a crisis the story has begun to proliferate and change online,” Mr. Hillmann said. “What we’re trained to do now is see who can get the message out the quickest along the broadest range of audiences.”

Write to Nick Niedzwiadek at nick.niedzwiadek@wsj.com