Michele Roberts backed the Los Angeles Clippers guard in a strongly worded statement, noting Paul's role in making her the first woman to head a North American major sports union last summer.
"Any suggestion that Chris Paul would ever conduct himself in a disrespectful manner towards women is utterly ridiculous, outrageous and patently false," Roberts said. "His personal management team, which includes several accomplished women who play a major role in virtually all of his business affairs, is, alone, evidence of that fact."
Paul, criticized Lauren Holtkamp on Thursday night after a loss at Cleveland, saying she might not be ready for the big leagues after six seasons in the NBA Development League. Holtkamp, who also has worked in the WNBA, is one of two active female officials in the NBA.
Lee Seham, general counsel of the National Basketball Referees Association, said in a statement his group reviewed Holtkamp's calls and "deems them fully justified."
"Furthermore," he added, "the NBRA deplores the personal and unprofessional comments made by Chris Paul. She belongs."
Paul was called for a technical foul by Holtkamp during the Clippers' 105-94 loss in Cleveland. Following a free throw by Cleveland with 10:17 left in the third quarter, the Clippers were attempting to inbound quickly when Holtkamp stepped in. Paul questioned her and was slapped with the technical.
"The tech I got was ridiculous," Paul said. "That's terrible. There's no way that can be a technical. We try to get the ball out fast every time down the court. When we did that, she said, 'Uh-uh.' I said, 'Why uh-uh?' and she gave me a technical. That's ridiculous. If that's the case, this might not be for her."
Questioning a referee's readiness is a common complaint the league hears about rookie officials. He likely will be fined for public criticism of an official but has the full support of the NBPA.
"Without hesitation, the Players Association stands firmly behind Chris, whose competitiveness may only be exceeded by the strength of his values and his convictions," Roberts added.
Paul also was supported by Becky Hammon, the former WNBA star who was hired by the San Antonio Spurs last year as the first full-time female assistant coach of an NBA team.
"Chris Paul is a competitor & he had an opinion, I don't think it had anything to do with the refs gender," Hammon wrote on Twitter.
The 34-year-old Holtkamp worked the D-League's championship series the last two years. A former player at Division II Drury University, she also officiated nine NBA regular-season games before her promotion to the full-time staff.
Violet Palmer is the league's other female referee, having worked about 900 regular-season games during a career that's in its 18th season.
Holtkamp wasn't scheduled to officiate Friday. Paul and the Clippers, who were assessed five technical fouls by Holtkamp's crew Thursday, were at Toronto on Friday night.
AP Sports Writer Tom Withers in Cleveland contributed to this report.