The three are suspected of having contracted the disease when they were bitten by mosquitos in Yoyogi Park in central Tokyo, officials said.
The patients - a man in his 20s in Tokyo as well as a teen and woman in her 20s in Saitama Prefecture north of the capital - go to the same educational institution in Tokyo.
None of them is in a life-threatening condition, officials said.
The last domestic infection of dengue fever was in 1945, although there are around 200 cases annually among those who have travelled abroad, mainly in Southeast Asia.
More From This Section
There is no vaccine or any specific medicine to treat dengue and patients should rest, drink plenty of fluids and reduce the fever using paracetamol or see a doctor, it says.
The disease is carried by the tiger mosquito, which are widespread across Japan.
Japanese officials say they have not detected the dengue virus in mosquitos caught in Yoyogi Park but they will disinfect areas where sufferers were bitten.
Yoyogi Park, which sits next to the grand Meiji Jingu Shrine and is one of central Tokyo's biggest public green spaces, is popular with Tokyoites and tourists alike.