Updated 3:53 p.m. ET

National Basketball Players Association executive director Billy Hunter was paid $3 million in salary during the fiscal year ending June 30, 2012, a 25 percent raise that went into effect with the start of last year's player lockout,  according to government filings. 

The filing with the U.S. Dept. Of Labor, first reported by USA Today, raised new questions about the finances and business practices of the union,  which already is under a business review and is the target of a U.S. Attorney's office investigation. 

Hunter, the longest-tenured union chief among the four major sports leagues, made $2.4 million in salary for the 12 months concluding June 30, 2011 -- the day before NBA owners imposed a lockout that lasted 149 days. Hunter's $600,000 raise, on top of payments to and business relationships with several family members that already have been made public, is expected to only fuel the uncertainty surrounding the union leader's future.

The NBPA declined comment on the labor filing, which was posted overnight on the Dept. of Labor website.

A review of the union's finances and business practices, being conducted by the New York firm Paul, Weiss, Rifkind, Wharton & Garrison, is not yet complete, league sources have told CBSSports.com. A concurrent probe by the U.S. Attorney's office also is ongoing.

The public scrutiny has been on allegations of nepotism stemming from union relationships with a financial firm where Hunter's son, Todd, is a partner; the employment of Hunter's daughter, Robyn, and daughter-in-law, Megan Inaba, on the union staff; and payments to a Washington, D.C., law firm that employs another of his daughters. Union president Derek Fisher raised questions about those and other issues after the lockout ended, but was rebuffed by the rest of the executive committee and asked to resign. He refused, and has no intention of stepping down with two years left on his term, sources said.

But the issues being examined by the law firm conducting the business review go beyond Hunter's rift with Fisher and the charges of nepotism, a person familiar with the probe told CBSSports.com. Hunter's salary, and the structure of the union constitution and bylaws that resulted in its approval, are among the other issues being examined, the person said.  

Regardless of the outcome of the business review and federal probe, sweeping changes are on the way for the players' association, which could have as many as seven of the nine seats on the executive committee up for election. On recent conference calls with committee members and player reps, union officials indicated that such elections could be postponed until All-Star weekend.

Details from the Dept. of Labor filings:

* Hunter's daughter Robyn, who is director of player benefits and concierge services, earned $89,695, up from $82,954 in the previous year. Inaba, Hunter's daughter-in-law, made $167,100 as director of special events and sponsorships -- about $6,000 less than the previous year.

* The NBPA paid Prim Capital, where Hunter's son, Todd, is a partner, $594,900 -- up about $20,000 from the previous year's filing. The law firm Steptoe & Johnson, which employs Hunter's daughter Alexis as special counsel, received $1.367 million for legal fees.

* The report included dozens of pages accounting for innocuous, routine union business, including the payment of each active player's $40,473 share of the 2011 BRI shortfall and millions in licensing funds from the NBA. Kobe Bryant, for example, received $259,000 in licensing money. Landry Fields received $16,668.

* Much of the report doesn't incriminate anyone and only would be of interest to, say, reporters who covered the lockout. For example, union economist Kevin Murphy's company was paid $351,029 in consulting fees from July 2011 through February 2012. David Boies' law firm, which handled the union's disclaimer strategy, was paid $221,167 from March 1-April 20 2012.

* The union paid Dewey & LeBoeuf, the since defunct firm of firebrand counsel Jeffrey Kessler, $1.319 million from July 2011 through January 2012. The union's cost for car services during the lockout was $142,154. During the 12-month period covered in the report, the NBPA paid $211,810 for public relations consulting to four firms.

* Hotels, as you might imagine, did quite well during the lockout. The NBPA paid three New York City hotels more than $100,000 each for lodging, catering and meeting rooms during and after the loclkout. The winner was the Sheraton on 53rd Street, host of several of the crucial meetings late in the negotiations and recipient of $168,852 from the union. The NBA, of course, incurred similar expenses but is not required to report them publicly since it is not a labor union.