An Air Self-Defense Force transport plane arrived in Djibouti from Juba on Thursday carrying four staff members from the Japanese Embassy in conflict-wracked South Sudan.
"I'm relieved. But I'm worried about the 20 to 30 Japanese nationals still in South Sudan," a female embassy official said upon arrival in Djibouti.
The four individuals looked tired but bowed their heads in appreciation when they arrived.
Defense Minister Gen Nakatani told reporters in India earlier in the day he had ordered the dispatch of the C-130 cargo plane to Juba to help evacuate the embassy staff.
Three C-130 planes from the ASDF's Komaki base in central Japan arrived in Djibouti late Wednesday for a possible rescue mission.
Chief Cabinet Secretary Yoshihide Suga issued the order in Tokyo on Nakatani's behalf.
Since clashes between forces loyal to President Salva Kiir and those loyal to Vice President Riek Machar broke out in South Sudan last week, 47 Japanese nationals including aid workers connected with the Japan International Cooperation Agency have been evacuated from the country to Nairobi in neighboring Kenya.
Around 20 Japanese nationals, most of them diplomats and embassy staff, had remained in Juba.
Reuters news agency reported that the vice president and his troops had left Juba by Tuesday to ease tensions and avoid further clashes that have so far left more than 270 people dead.