The New York Liberty were fined $500,000 for chartering flights to away games during the second half of the season and for other violations of league rules.
The flights were purchased by the owners of the Brooklyn Nets and the Liberty, Joe and Clara Tsai.
The news was first reported by a magazine.
In October, Tsai said he was working with airlines and the league to find a charter sponsor for the players.
Chartering is not allowed in the WNBA because it would create a competitive advantage for teams whose owners can afford it. While she supports the idea of teams chartering, the league needs to experience more financial growth to be able to cover those expenses.
The WNBA discovered that he was secretly chartering flights for the Liberty while he worked to find a solution for all of the franchises. Liberty players posted on social media about their trip to Napa. The Liberty spearheaded an unofficial proposal that the Board of Governors rejected, in which the league would get comped for three years of flights.
A spokesman for the WNBA denied that concrete had been presented.
A spokesman for the New York Liberty said that there was no proposal to offer three years of charter flights for the teams. That has not happened to date.
The Chicago Sky and Phoenix Mercury were the most recent teams to be paid for travel across multiple time zones by the WNBA.
The league's general counsel suggested a number of severe punishments for the Liberty, including losing every draft pick, suspending ownership, and even ending the franchise.
Commercial travel for WNBA teams has been a major flash point for the league in recent years, as players have drawn attention to cramped, uncomfortable seating on flights, and travel gaffes that have even led.
The news of the fine caused an uproar on social media.
The Liberty's franchise player, Sabrina Ionescu, wrote on social media that the league's handling of the situation was a joke.
The league that fined the players for standing up for social justice was the same one that fined the teams for standing up for equity.
Ramona Shelburne contributed to the report.