A television cameraman was killed when the anchored ferry sank near Jakarta after 16 officials from the national transport safety board, police and journalists went on board on Sunday.
Soon after the party boarded, the vessel listed sharply and sank within five minutes, witnesses said.
Rescuers were searching for another cameraman and two police officers who were still missing, Colonel Didin Zainal Abidin, who co-ordinates the navy rescue team, said on Monday.
A reporter was in hospital in serious condition.
Abdullah Azwar Anas, the member of parliament, said Sunday's incident "was extremely embarrassing".
Bima Marzuki, an RCTI television reporter,
was injured when the ferry sank [Reuters]
"It was extremely embarrassing and it was sheer recklessness," he was quoted as saying by Antara news agency.
At least 42 people died in last week's fire on board the Levina I which broke out soon after dawn on Thursday as the ferry headed from Jakarta to Bangka island off Sumatra.
On Saturday the scorched hulk was towed to just a few kilometres from Jakarta's main port.
Setyo Rahardjo, chairman of the National Transport Safety Commission, said the sinking was unexpected.
"We did not think about the possibility of the ship sinking because it was just fine when it was towed 50 miles in the sea," he said.
He added that officials had boarded the vessel only after a clearance from marine police that it was free from gas.
Warned of danger
But Colonel Didin said journalists had been warned of the danger of going on board and told to wear life jackets but some had refused.
"There was a briefing, there was a warning from the port administrator that the ship was dangerous," he said. "Some journalists refused to wear life vests, saying they were cumbersome. It was a pure accident."
Preliminary findings suggest the ferry caught fire after a blaze in a truck carrying inflammable chemicals on the lower deck.
About 300 people are known to have survived the blaze, but about 100 people are still thought to be missing, although the actual number remains unclear because some passengers were apparently not listed on the official manifest.
The government has revoked the ferry operator's licence for failing to list children on the manifest.