"We're following up, actually, today, with some interviews to various personnel so that we'll, hopefully, have all the facts in the next couple of days and be able to make some decisions later this week," Goodell said Monday.
Jets general manager Mike Tannenbaum said last Thursday his team should have included Favre's torn biceps tendon on mandatory weekly injury reports over the final third of last season. Favre is now with the Minnesota Vikings.
Past violations of that nature usually have resulted in fines.
In 2007, the NFL began requiring teams to list the level of a player's participation in practice on Wednesday, Thursday and Friday for a Sunday game and on Friday list his playing status (probable, questionable, doubtful or out) for that week's game. For a Monday night game, practice participation must be listed for Thursday, Friday and Saturday with his playing status listed on Saturday.
Teams also must identify injuries in some detail; an arm injury must be listed more specifically, such as a shoulder, elbow, wrist, hand or muscle.
"There frequently have been charges, including from the media, that the injury reports weren't done accurately, and so we've always followed up on that," Goodell said before Monday night's game between the New England Patriots and the Buffalo Bills.
"It appears that we have some facts" in the Favre case, he said. "Obviously, the Jets came out and said it wasn't handled properly so we'll follow up on that, make sure that it's done properly and we understand the facts, and then we'll issue a discipline as a part of that."
Tannenbaum said he should have listed the quarterback as "probable," but didn't because the injury was not severe enough to require daily treatment and there was never any doubt Favre would play.
The case is an opportunity to stress that all teams must abide by the injury report rules, Goodell said.
"We establish policies. They're to be followed. And all 32 clubs are going to be held accountable for that and, unfortunately, when someone violates it, the other 31 know that," he said. "You can bet on that."
After last season, the NFL made it a penalty for a defender knocked down by a blocker to lunge at a quarterback and drive a head or shoulder into the quarterback's lower leg. Patriots quarterback Tom Brady suffered a season-ending knee injury on such a play in last year's opener.
He was back for Monday night's game.
"We're thrilled he's back," Goodell said, "but we feel that way about all our players. We'd love to see all of our players on the field as much as possible. That's why we put so much focus on our players' safety rules."
The commissioner was winding up a busy stretch of season openers.
He attended Thursday night's game between the Tennessee Titans and the Steelers in Pittsburgh, then went to Green Bay for Sunday night's game between the Packers and the Chicago Bears. The Bills-Patriots game was one of two Monday night openers, preceding the San Diego Chargers game at the Oakland Raiders.
Defensive end Richard Seymour was traded Sept. 6 to the Raiders by the Patriots for a 2011 first-round draft pick. He didn't report until Friday, saying he was "blindsided" by the deal and had to take care of family matters.
"It was handled properly. I think Richard has made himself clear about the [personal] issues he had to deal with," Goodell said. "We understand that, and he's a class act and he's honoring his contract and he's there with enthusiasm."
Goodell wasn't as upbeat on progress toward a collective bargaining agreement to replace the one that expires after next season. He said he was neither encouraged nor discouraged.
"We have a lot of work to do," he said. "We're going to get to it, hopefully bang something out."