He joined the Republic of Fiji Military Forces in 1982 and served in the Fiji Navy.[1] In 1994 he was the Captain of the newly commissioned RFNS Kula.[2] During his time in the military, he served as the Commander of Fiji Navy, Director Finance and Logistics and Commander.[1] While serving as Navy Commander, Naupoto was arrested drink-driving. His case file subsequently went missing from the Nabua police station,[3] but was eventually found, and he was convicted and fined US$100.[4]
Following the 2006 Fijian coup d'état Naupoto was appointed Director of Immigration by the military, and was responsible for placing travel bans on the regime's opponents.[5] He also deported legal representatives of regime opponents.[6] After being sent to India for training,[7] he was appointed Permanent Secretary in the Prime Minister's Office,[8] and then chair of the Fiji Trade and Investment Board[9][10] and Permanent Secretary of the Department of Fisheries and Forests.[11] In February 2012 he was appointed Minister of Youth and Sports in the military cabinet.[12]
Naputo was selected as a FijiFirst candidate for the 2014 Fijian general election,[13] but not elected. Following the election he returned to the military, serving as chief of staff.[14][15] Following the sudden resignation of RFMF Commander Mosese Tikoitoga in August 2015 he was appointed acting commander.[16] The appointment was made permanent in March 2016.[17][18] In November 2015 he was promoted to Rear Admiral.[19] When Jioji Konrote was elected President of Fiji in October 2015, Naupoto became eligible for a seat in Parliament as his replacement, but turned it down to stay in the military.[20] He retired from the RFMF in March 2021,[21] and was replaced as RFMF Commander by Jone Kalouniwai in September 2021.[22][23]
He was selected again as a FijiFirst candidate for the 2022 election,[24][25] and was elected with 830 votes.[26][27] Following the election he was appointed as chair of the Foreign Affairs and Defence Committee.[28]
In November 2014 Naupoto was made an Officer of the Order of Fiji.[29]
Following the collapse and deregistration of FijiFirst he remained in parliament as an independent, but said that he would support the government of Sitiveni Rabuka.[30]