"I want to emphasize, we have made no judgement on these points. And we will not compromise the investigation by engaging in speculation."
Goodell confirmed the footballs were tested at halftime of the AFC championship game.
Once the investigation is complete, the results will be shared publicly, according to Goodell.
Goodell was also asked about Seattle Seahawks running back Marshawn Lynch's comments at Media Day on Tuesday, during which the player repetitively said, "I am just here so I won't get fined."
"Marshawn understands the importance of the Super Bowl," Goodell said. "I've been very clear that when you're in the NFL you have an obligation to the fans."
"It is part of your job. And there are things we all have to do in our jobs that we may not necessarily want to do," he added.
"It may not be at the top of his list. Everyone else is cooperating and doing their part. It is our obligation," Goodell said. "It comes with the territory. It comes with the privilege of playing."
Looking to the off season, Goodell said the league will focus is on player safety, including establishing a Chief Medical Officer position to oversee medical-related policies.
Goodell said he expects to have the position "in place very soon."
Goodell added that concussions were down 25 percent this season, continuing a three-year trend.
The league also aims to bring more awareness to domestic violence and sexual assault, Goodell said.
This past Thursday was the first meeting of the new League Conduct Committee to review the personal conduct policy, of which Goodell said "raises the standards for all of us" by emphasizing ongoing education, prevention and support services.
"We want to make a difference, not just internally but externally."
Looking back on this season, Goodell said the league is in a better place than it was in August.
"We obviously as an organization have gone through adversity," he said, but noted that "the NFL is made up of good and caring people."
"It's been a tough year but a year of progress," Goodell said.