Steve Simon, CEO of the Women's Tennis Association, said the tour's policy was in line with Olympic standards, which state that male-to-female trans athletes can compete without gender reassignment surgery, subject to a maximum testosterone level.
"The WTA has always been an organisation based on acceptance and providing people equal opportunity," Simon said by phone from the official launch of this year's WTA Finals in Shenzhen, China.
"Right now our policies do provide for (transgender players)," he added. "They are not necessarily in line with Martina's position.
"But we respect all the various opinions... she's looking for the topic to be debated further and I think it's a very fair position to be taking."
Navratilova, winner of 18 Grand Slam singles titles, was condemned as "transphobic" after she wrote in a newspaper column that letting men who "decide to be female" compete with women is "insane and it's cheating". She later apologised.
This week British former Olympic swimmer Sharron Davies also voiced opposition to transgender athletes competing in women's sport.
"I believe there is a fundamental difference between the binary sex you are born with and the gender you may identify as," Davies tweeted.
"To protect women's sport those with a male sex advantage should not be able to compete in women's sport."
Meanwhile Simon backed world number one Naomi Osaka to overcome her struggles in the public eye after her rapid rise to prominence.
Osaka, 21, has squirmed in the spotlight and after splitting with her coach and losing to Kristina Mladenovic in Dubai, she tearfully complained that "people are staring at me, and not in a good way".
"I think it's natural for any person to have to deal with those emotions and expectations and the pressure that brings, especially when you're young," Simon said of the US and Australian Open champion.
"But Naomi is certainly a very strong person. I think she has the personality and perseverance to work her way through it and I think she will get more comfortable as we're going forward."
Simon added that he was excited to be embarking on an unprecedented, 10-year deal for the WTA Finals in Shenzhen, with record prize money of $14 million.
It caps a strong end-of-season swing on Chinese territory, which now boasts more WTA tournaments than the United States. China also has four top-50 players including Wang Yafan, who won her first WTA title this month in Acapulco.
"I think it's important that we have players from this region that are competitive," he said.
"Clearly there's a pool here and it seems to be growing. There's more and more of them seeing various levels of success."