The former world No1 previously underwent treatment for early-stage breast cancer in 2010.
Navratilova, 66, will not be able to fly to the Australian Open later this month, where she was due to work as a TV pundit.
“This double whammy is serious but still fixable,” she said in a statement. "I’m hoping for a favourable outcome. It’s going to stink for a while, but I’ll fight with all I have got.”
She later thanked her fans for all their support and insisted that she is “not done yet”.
She wrote on Twitter: “Needless to say my phone and twitter are both blowing up so I will say again – thank you all for your support and I am not done yet :).”
Navratilova dominated the sport in the 70s and 80s, winning 59 Grand Slam titles: 18 singles, 31 women’s doubles and 10 mixed doubles.
In a statement, her representatives said that both the stage one cancers have a “good” prognosis and that Navratilova hopes to continue to work as a pundit for the Tennis Channel of this month’s Australian Open remotely from her home in Miami as she recovers.
The cancer was first discovered in early November during the WTA Finals when Navratilova noticed a swelling in her neck.
A statement added: “When it didn’t do down, a biopsy was performed, the results came back as stage one throat cancer.
“At the same time as Martina was undergoing the tests for the throat, a suspicious form was found in her breast, which was subsequently diagnosed as cancer, completely unrelated to the throat cancer.
“Both of these cancers are in their early stages with great outcomes.”
The ex-world number one, who married model Julia Lemigova in 2014, previously underwent treatment for early stage breast cancer in 2010.
A routine mammogram revealed the Czech-US star had developed a ductal carcinoma in her left breast.
She had the tumour surgically removed before receiving radiation therapy.
The nine-time Wimbledon singles champion said she felt “helpless” after first being diagnosed. But she decided to go public with her news to help other women suffering similar health problems.