He said authorities had received little word of what happened in the Donggala area near the epicenter of the quake, where almost 300,000 people live.
Philippine Ambassador to Indonesia Leehiong Wee said the unidentified Filipino was a detainee serving his sentence at Lapas Penitentiary in Palu.
A magnitude 7.5 quake spawned a deadly tsunami on Friday evening, killing more than 400.
Original reports had placed the death toll at around 48 people.
Three French nationals and a South Korean, who may have been staying at a flattened hotel, had not yet been accounted for, it added.
Desperate survivors, now facing a third straight night sleeping outdoors, turned to looting shops for basics like food, water and fuel as police looked on, unwilling or unable to intervene.
Meanwhile, the Thai embassy in Jakarta is examining ways to help Thai nationals who may have been affected by the disaster, according to a post on the embassy's Facebook page.
Earlier this year, a series of powerful quakes hit Lombok, killing more than 550 people on the holiday island and neighbouring Sumbawa.
Hundreds had gathered for a festival on Palu's beach when the wall of water smashed onshore at dusk, sweeping many to their deaths.
Injured people are treated outside at Army hospital following earthquakes and a tsunami in Palu, Central Sulawesi.
Anthonius Gunawan Agung, 21, was the only person left in the control tower at the Air Traffic Tower of Mutiara Sis Al Jufri Airport in Palu when the magnitude-7.5 quake struck the coastal city on Friday.
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Finance Minister Sri Mulyani Indrawati said the government had allocated 560 billion rupiah ($37.58 million; more than 1.2 billion baht) for disaster recovery, media reported.
Sutopo said 821 of those killed were in the city of Palu.
With Palu airport closed, relief workers have to make their way to Palu by road. Seawater still pooled inland and a mosque heavily damaged by the quake was half submerged.
Pope Francis has led the faithful in prayer for the people of Sulawesi hit by the natural disaster and tsunami. "We're now getting limited communications about the destruction in Palu city, but we have heard nothing from Donggala and this is extremely worrying". Many people were trapped and buried under collapsed houses.
Looters hit a badly damaged shopping mall, apparently unconcerned for their safety amid ongoing aftershocks and the structure's questionable stability.
Donggala town has been damaged badly, according to a reporter on the scene.
Help and supplies are being flown from Indonesia's capital city Jakarta to the island of Sulawesi.
The initial quake struck as evening prayers were about to begin in the world's biggest Muslim majority country on the holiest day of the week.
"The tsunami didn't come by itself, it dragged cars, logs, houses, it hit everything on land", Nugroho said, adding the tsunami had travelled across the open sea at speeds of 800 kph (500 mph) before striking the shoreline.
The Philippines was "ready to respond and extend assistance to Indonesia", Cayetano said from NY, where he was attending the 73rd Session of the United Nations General Assembly.
Indonesia, which sits on the seismically active Pacific Ring of Fire, is all too familiar with deadly earthquakes and tsunamis.