The Dallas Morning News reported that family court Associate Judge Randall Grubbs ordered the tests on Cristal Taylor, who claims Nowitzki is the father of her unborn child.
Medical records show that Taylor, 38, is pregnant, but Grubbs wanted his own test, according to the Morning News.
The test and results will determine whether DNA testing is necessary as Nowitzki seeks sole custody of the child Taylor claims to be carrying.
"We know the first one has to happen," Grubbs said during a hearing on Friday, according to the Morning News. "The other one may be moot."
In addition, Grubbs sealed the proceedings; attorneys told the newspaper they could not comment.
Taylor was arrested May 6 at Nowitzki's home in Dallas on a 2006 theft of services charge in Beaumont, Texas, for allegedly failing to pay for $10,000 worth of dental work.
She was transferred on June 30 to a jail in St. Charles, Mo., because of probation violations in a 1997 forgery and stealing case. She remains in that jail, after a judge refused to lower her $25,000 cash-only bond during a hearing on July 6. Her next hearing in that case is Aug. 24.
Taylor's St. Louis attorney, Matthew Fry, had argued that Taylor should be released because she needed outside medical care for a pregnancy that was deemed "higher risk," the Morning News reported in July.
St. Charles Circuit Court Judge Nancy Schneider said she saw no reason Taylor's medical needs couldn't be taken care of in jail, and added that while she was not doubting Taylor's pregnancy, "It is my understanding these [health screening reports] are self-reported by an inmate," the newspaper reported.
Attorney Scott Renick of Beaumont said he only represents Taylor on the criminal matter in Texas and declined comment on the case involving Nowitzki.
Information from The Associated Press was used in this report.