The 23-year-old man was seized on Monday as he travelled alone around the area, foreign ministry officials said.
The student called the Japanese embassy in Tehran to say he had been captured, Kyodo news agency reported.
Japanese Foreign Minister Masahiko Komura said he had asked his Iranian counterpart, Monouchehr Mottaki, for help to resolve the matter.
“He said they have identified the whereabouts of the abductee and he told me he will make efforts to resolve the issue,” Mr Komura told journalists.
The student, whose identity has not been released, crossed into Iran after travelling in Pakistan, Kyodo said.
There have been a series of abductions targeting foreigners in Iran’s lawless south-eastern region.
The area is a conduit for gangs smuggling drugs from Afghanistan and Pakistan.
In August, two Belgians tourists were seized in the area. Both have now been released.
