Boston will refund millions of dollars in “impact” fees it collected from marijuana companies, the first Massachusetts municipality to do so after state lawmakers enacted a measure cracking down on the controversial payments.

Officials in Mayor Michelle Wu’s administration notified local cannabis operators of the decision in a letter sent on Nov. 3, saying they would stop collecting the fees — worth 3 percent of each firm’s annual revenue and ostensibly meant to offset their negative effect on the surrounding community — and return all the money collected since recreational sales began in the city more than two years ago.

In a short statement, a city spokesperson said nine Boston marijuana companies would receive checks totaling $2.86 million, with some of the money coming from unexpended fees and the remainder from a “legal reserve fund.”

“The city determined this was the appropriate course of action after reviewing the recent changes to state law,” the spokesperson said.

Since 2017, Massachusetts law has allowed cities and towns to charge local marijuana operators impact fees of up to 3 percent of their revenue, as long as the payments were “reasonably related” to the facility’s negative impacts.

But in the absence of enforcement, most cities and towns charged the maximum rate, or even more, without enumerating any issues. They also spent the funds on a variety of projects, many with little apparent connection to the presence of pot shops and growing facilities.