His entry into the ruins came thanks to a special request he submitted while stranded since mid-March in the town of Aguas Calientes, on the slopes of the mountains near the site.
Minister of Culture Alejandro Neyra said the Japanese tourist was able to visit alone, together with the head of the park, before returning to his home country.
Jesse Takayama, his entry ticket on hand since March, entered the ruins of the citadel built more than 500 years ago on Saturday.
He became the first visitor in seven months to be able to walk through the world heritage site.
His original plan had been to spend only a few days in Peru to take in Machu Picchu.
“This is so amazing! Thank you!” said Mr Takayama in a video recorded on the top of Machu Picchu mountain.
Minister Neyra said that in November the stone ruins of Machu Picchu will be reopened for national and foreign tourists, without specifying the date.
The site will permit 30 per cent of its normal capacity of 675 people per day.
“We are still in the middle of a pandemic,” Mr Neyra said. “It will be done with all the necessary care.”