"Inna lillahi wa inna ilaihi rojiun. Our condolences on the passing of Mr Sutopo Purwo Nugroho in Guangzhou, in the wee hours today," the President wrote on his official Instagram account on Sunday.
Sutopo who was included in the list of "The Asians of the Year 2018" by the Straits Times died at 49 while being treated for lung cancer in China.
Jokowi said Sutopo had still shown his dedication to the nation and the public by kept providing the latest information on disasters happening in several regions in Indonesia, despite his illness.
Earlier, the BNPB announced that it suffered a tremendous loss in the passing of Sutopo, who had been confirmed by doctors to get lung cancer in December 2017. The cancer that he suffered had spread to his body's bones and several other vital internal organs.
His remains would be flown by a Garuda Indonesia aircraft from Guangzhou to Soekarno-Hatta International Airport, Cengkareng, Indonesia, on Sunday at 03:45 p.m. local time, Indonesian authorities said.
The Garuda Indonesia aircraft serving flight number GA-899 was expected to arrive at the Cengkareng-based airport at about 08:30 p.m. local time, General Manager of Garuda Indonesia's Guangzhou Office Suzana Argentine Walandouw said.
The Indonesian Consulate General in Guangzhou also confirmed the Garuda Indonesia officer's information on the repatriation of Sutopo's remains.
"May everything go smoothly," Walandouw said, adding that late Sutopo's wife Retno Utami Yulianingsih and several relatives would also join the same flight. Shortly after arriving, Sutopo's remains would be carried to the mourning house.
From the mourning house, which is located at Tapos, in Depok city, West Java Province, Sutopo's remains would then be transported to Boyolali in Central Java Province for burial.
Indonesian Foreign Minister Retno LP Marsudi had contacted Sutopo's wife to express her condolences.