Citing a source, Golf.com reported that Johnson has failed three drug tests -- two for cocaine (in 2014 and '12) and one for marijuana (2009).
Johnson, 30, was suspended for the 2012 failed test, Golf.com reported, but that suspension was never made public. Under its guidelines, the PGA Tour is not required to announce any disciplinary actions against players who test positive for recreational drugs.
Johnson announced Thursday that he was taking a leave of absence from competition, effective immediately, for "personal challenges."
The PGA Tour released a statement Thursday wishing Johnson well. On Friday, PGA Tour executive vice president Ty Votaw refuted the report, reiterating that the leave is voluntary and saying Johnson has not been suspended.
"With regard to media reports that Dustin Johnson has been suspended by the PGA Tour, this is to clarify that Mr. Johnson has taken a voluntary leave of absence and is not under a suspension from the PGA Tour," Votaw said in a statement.
Votaw also responded to a request for comment from ESPN.
"In regard to the report in golf.com, the PGA Tour does not comment on rumors and speculation," he said.
Johnson will miss next week's PGA Championship in Louisville, Kentucky, as well as the FedEx Cup playoffs and the Ryder Cup.
His biggest sponsor, TaylorMade-Adidas, also would not comment.
"TaylorMade-Adidas Golf will not comment on allegations," the company said in a statement. "We support Dustin Johnson's decision to temporarily step away from the PGA Tour."
Johnson played the Cadillac Championship in March 2012 and then did not play again until the Memorial in late May 2012. He said then he was not playing because he'd injured his back lifting a jet ski. But Golf.com's source says Johnson was actually serving a suspension for failing a drug test for cocaine. At the time, the tour had no official comment, and Johnson's agent denied that the player had been suspended.
The PGA Tour began drug testing in July 2008.
One year later, PGA Tour commissioner Tim Finchem was asked to confirm that there had been no positive tests in the first year from either recreational or performance-enhancing drugs. He drew a distinction between the two.
"I said we have had no positive tests with respect to performance enhancing. We may have had some test results that trouble us in other areas that we treat in a different bucket," Finchem said in July 2009. "But we don't publicize those. We treat those as conduct unbecoming. If we get a test like that, we will consider it conduct becoming, and what are our choices? We can suspend a player. We can fine a player. We can do both of those and put a player into treatment."
Johnson is not the first player to take a leave of absence.
John Daly announced in September 1994 that he was taking the rest of the year off because of "mental and physical" problems. In announcing Daly's decision, Finchem repeatedly used the word "voluntary," but said the decision was reached after numerous meetings between Daly and the tour.
Daly said Friday evening he could not recall details from 20 years ago. He said of Johnson, "I hope he's all right."
Daly most recently was suspended in 2008 following a tumultuous year of off-course incidents. He called The Associated Press to say he had been suspended for six months because "I'd rather be honest, especially with the fans."
The tour, told that Daly had confirmed his suspension, declined comment citing its longstanding policy on not discussing discipline.
Meanwhile, the PGA of America issued a new Ryder Cup points list Friday that removed Johnson from the standings. He had been No. 5, virtually certain to be an automatic selection when qualifying ends after the PGA Championship next week.
Information from ESPN's Mark Schwarz and Darren Rovell and The Associated Press is included in this report.