The 'Born to Die' singer had been booked to play a concert in the country earlier this year, but postponed the show until May.
Reps for the star have released a statement apologising to fans for yet another cancellation of the show.
The statement reads: "It is with great regret Lana will not be performing in Tokyo today. She is suffering from exhaustion and the show had to be cancelled.
"Lana says, 'I am really sorry to not have made it over to Japan again, I would love to be there to sing and look forward to performing a show that the fans deserve'."
Del Rey later sent another message via her Twitter account apologising, saying: "Wish I could be with everyone in Tokyo but I'm really sorry I am sick. Thinking of you and I will come back soon."
This is not the first time Del Rey has cancelled scheduled shows. In January, she pulled out of a show for MTV in London due to an unspecified illness. She later cancelled a tour after her badly received performance on Saturday Night Live.
The 25-year-old recently confirmed the release of her fourth single 'National Anthem' on July 8.
Watch Lana Del Rey's video for 'Blue Jeans' below: