Ferry operator Batamfast revealed last week that it is conducting a review of its emergency response procedures, and will involve third-party consultants if necessary.
However, it also insisted that its evacuation resources on its ferry Sea Prince, including life rafts which can fit 65 people each, were in "full working order" when it struck an object in Indonesian waters last Sunday night on its way to Singapore from Batam.
Mr Chua Choon Leng, passage operations manager at Batamfast, also told The Sunday Times: "I know passengers online are complaining that the rescue process took such a long time.
"But I think we put in as much effort as we could - considering how dark it was at night - and managed to transfer the passengers within two hours."
He stressed that no one was injured and all 97 passengers were accounted for.
He revealed that Batamfast is assisting the Singapore and Batam authorities in investigations, and four of the seven crew members on board Sea Prince - the captain, the chief deck officer and two engineers - have been interviewed.
Batamfast also said that all its equipment undergoes regular testing to comply with local port state and international Safety of Life at Sea (Solas) requirements, adding that its crew members are "highly trained in the standard operating procedures in the event of accidents on voyage".
In response to queries, the Maritime and Port Authority of Singapore (MPA) said that Indonesia's National Transportation Safety Committee will be conducting an investigation, as required by the International Maritime Organisation's Casualty Investigation Code.
This is because the incident occurred in Indonesian waters and involved an Indonesia-flagged vessel and crew, a spokesman said, adding that Singapore and the MPA will assist the Indonesian authorities in the process.
She said the investigation, which may take up to a few months depending on its complexity, aims to "identify the causes of the incident and prevent future incidents".
The last incident in Singapore waters occurred in June 2011, when a Belize-registered passenger ferry, FB Falcon Princess, was travelling from Changi Ferry Terminal to Tanjung Belungkor Ferry Terminal in Johor.
It encountered an engine problem and beached north of Pulau Tekong. The incident did not result in any injuries or pollution.
This year, there are 47 ferries plying the route between Singapore and Batam. Last year, the figure was 48.