A league spokesman confirmed the investigation, which was first reported Sunday by television station WTHR in Indianapolis, to ESPN on Monday morning.
Patriots coach Bill Belichick said Monday afternoon that the organization will "cooperate fully with whatever questions they ask us and whatever they want us to do." He added that the first time he heard about the issue was Monday morning.
"I can't imagine," he said in an interview later Monday with Boston radio station WEEI. "I really don't know what to say or know anything about what we're talking about here. Whatever it is, we'll cooperate with them the best we can."
Patriots quarterback Tom Brady laughed when asked about the report.
"I think I've heard it all at this point ... it's ridiculous," Brady said Monday morning during his weekly interview with WEEI. "I don't even respond to stuff like this."
Citing a person familiar with the background of the matter, Newsday reported Monday that the Colts first noticed something unusual after an interception by Colts linebacker D'Qwell Jackson late in the second quarter.
Newsday reported that Jackson then gave the ball to a member of the Colts' equipment staff, who noticed the ball seemed underinflated. At that point, coach Chuck Pagano and general manager Ryan Grigson were notified, and Grigson alerted NFL director of football operations Mike Kensil, according to the report.
Pagano said he did not notice issues with the football, and he didn't specify when asked whether the Colts had reported the issue to officials.
"We talk just like they talk to officials [before the game], we have an opportunity to talk to the officials about a lot of things, things that you've seen on tape like the formations we talked about last week," Pagano said. "Every coach in the league gets an opportunity to visit with the officials about that kind of stuff before the game."
An underinflated football could be easier to grip and catch. NFL rules stipulate that footballs must be inflated between 12.5 and 13.5 pounds per square inch and weigh between 14 and 15 ounces.
Former NFL official Jim Daopoulos, in an interview with ESPN on Monday morning, explained the process in which footballs are managed. Two hours and 15 minutes before each game, officials inspect 12 footballs from each team and put a mark on them to indicate they meet the proper requirements and are good for usage. Then those footballs are given to the ball attendant.
"I think I've heard it all at this point ... it's ridiculous. I don't even respond to stuff like this."
Tom Brady, to WEEI, on report that Patriots intentionally deflated footballs
in AFC Championship Game vs. Colts
There also is a second set of six footballs, used specifically for the kicking game, that are marked appropriately and remain in the possession of officials at all times.
"Officials check balls as they go into the game, and if the ball doesn't feel perfect, they can throw it out," Daopoulos said. "There is always the possibility that balls can lose air due to the conditions."
A team can be fined if it is found to be knowingly altering the weight of the football.
The NFL's game operations manual states: "Once the balls have left the locker room, no one, including players, equipment managers, ball boys, and coaches, is allowed to alter the footballs in any way. If any individual alters the footballs, or if a non-approved ball is used in the game, the person responsible and, if appropriate, the head coach or other club personnel will be subject to discipline, including but not limited to, a fine of $25,000."
Heavy rain began falling at Gillette Stadium in the second half of Sunday's game. New England owned a 10-point lead at halftime before pulling away in the second half, scoring three third-quarter touchdowns en route to a 45-7 victory over the Colts.
On the first offensive play from scrimmage in the third quarter, following a kick return, referee Walt Anderson briefly stopped play to replace a football which could have been related to this issue.
"We try to do things the right way," Patriots special teams standout Matthew Slater said. "We work hard at our jobs, at our professions to be successful. It's unfortunate that things like this come up. That's life. That's the world we live in."
Tight end Rob Gronkowski, meanwhile, echoed his quarterback in taking a humorous approach to claims that the Patriots used underinflated footballs. He attributed it on Twitter to his penchant for spiking footballs after touchdowns.
Whoops lol pic.twitter.com/uLxN7A5cpq
— Rob Gronkowski (@RobGronkowski) January 20, 2015
ESPNBoston.com's Lee Schechter and The Associated Press contributed to this report.