The law enforcement official said the bets involved thousands of dollars and were made on games during the 2005-2006 and 2006-2007 seasons.
The NBA issued a brief statement Friday: "We have been asked by the FBI, with whom we are working closely, not to comment on this matter at this time."
The FBI probe, which began recently, also involves allegations that the referee had connections to organized crime associates. Other arrests are expected, the official said.
The referee had a gambling problem, according to the official, and was approached by low-level mob associates through an acquaintance.
The investigation first was reported Friday by the New York Post.
"I'm shocked, terribly shocked," said Gary Benson, NBA official for 17 years, who retired two years ago because of knee problems. "Those are people that you work with and that you literally -- you spend more time with those people than you do with your family."
Nevada gambling regulators were not involved in an investigation and had no information about the allegations, said Jerry Markling, enforcement chief for the state Gaming Commission and Gaming Control Board.
Markling, in Las Vegas, said he learned of the probe from news accounts.
"The allegations were new to us," said Mark Clayton, a control board member. "However, we will continue to monitor them to ascertain whether there is any connection to Nevada's licensed sports books."
Veteran oddsmaker John Avello, at the Wynn resort on the Las Vegas Strip, said that without specific information it would be difficult to identify wagering irregularities over the last two seasons.
"At this point, it's too early to know if any games were affected," Avello said, adding that no regulators or investigators had contacted him about the case.
Jay Kornegay, executive director of the sports book at the Las Vegas Hilton, said he had never seen any unusual activity in NBA betting, and was surprised not to have heard about an investigation until Friday.
"Whispers would have happened on the street, and we would have heard something," Kornegay said. "Any type of suspicious or unusual movements, you usually hear in the industry. We're so regulated and policed, any kind of suspicion would be discussed.
"We haven't seen anything like that in the NBA that I can remember," he said, "and we haven't been contacted by anybody."
Kornegay said legal sports betting in Nevada represents a fraction of sports betting worldwide, with 98.5% of all action taken outside the state. Clayton cited a 2005 estimate by the National Gambling Impact Study Commission that found $380 billion is wagered on illegal sports betting, compared with $2.25 billion in legal sports betting in Nevada.
Gambling long has been a problem in sports, and leagues have made a point of educating players of the potential pitfalls. The NBA, for example, discusses gambling at rookie orientation, even bringing in former mobster Michael Franceze to speak.
NBA commissioner David Stern had long objected to putting a team in Las Vegas because it permits betting on basketball, though earlier this year allowed Mayor Oscar Goodman to submit a proposal to owners on how the city would handle wagering on a team if it moved there.
Goodman argues that legalized gambling, monitored by the Nevada Gaming Commission, prevents these types of suspicious activities.
"We're the only regulatory agency in the world that really looks at unusual activity as far as the movement of the line and that type of conduct," he said. "I think it's a good thing that Las Vegas has the type of regulation that makes sure that bad things don't happen."