Slamet Riyadi also said by telephone on Tuesday that there were just 66 people on the ferry - 60 passengers and six crew - and not around 100 as officials had feared earlier.
"Just one passenger has yet to be found," he said.
The boat was travelling from a port on Ndao island to nearby Rote island when it capsized late on Monday, according to Bambang Julianto, the port chief in Kupang, the capital of West Timor and the area where the mishap took place.
The Indonesian navy had dispatched one ship and an airplane to search for the boat which ran into problems late on Monday near Rote Island, 1,900km east of the capital Jakarta.
It is often difficult to determine how many passengers are aboard Indonesian ferries, since they frequently carry individuals who have not paid for tickets or are not listed on manifests.
A ferry sank in heavy seas in the same area less than three months ago, killing at least 10 people. More than 100 were rescued.
Earlier reports said 19 survivors had been taken to a hospital on Rote island, while the other survivors were on a beach on Ndao island.
The small motorised boat sank in rough seas, possibly because it was overloaded.
Ferries are a popular means of transport between the more than 17,000 islands of Indonesia, where sea connections are cheaper and more available than air routes.
But safety standards are not strictly enforced and many ferries are overcrowded.