Divers are still searching for 17 people still missing from Sunday's fire.
"We have detained the captain of the boat, and are now taking his statement," Jakarta's maritime police director, Hero Hendrianto Bachtiar, told CNN Indonesia.
He said that three crew members and two port authority staff were in police custody.
At a press conference, Antonius Tonny Budiono, director general for sea transportation at the Indonesian ministry of transport, addressed reports that the captain was the first to leap off the Zahro Express ferry when it caught fire.
"A captain who abandons ship first is no captain at all," he said, according to CNN Indonesia. "A captain's obligation is to be the last person off the ship, after all the passengers have been evacuated."
He said that the captain would face severe sanctions, including the revocation of his sailing permit.
Divers hunt for missing
The New Year's Day tragedy unfolded a short distance away from Muara Angke port at 9 a.m.
The boat was on its way to the tourist destination of Pulau Tidung Island in North Jakarta when it caught fire. Most of the 200 plus passengers were Indonesians celebrating the New Year's holiday, according to local media reports.
"Tomorrow, we will deploy five divers to find the missing passengers. We will assure if there are still victims in the waters," the Ministry of Transport's director of sea and coast surveillance, Victor Vikki Soebroto, said at a press conference Sunday evening.
Some 194 people were saved but 17 are still missing, an officer at the Disaster Mitigation and Control Operation Center, Seply Madreta confirmed to Antara, an official news agency.
The cause of the fire is unknown.