NZ Transport Agency director of rail safety Celia Patrick said two new restrictions were now, temporarily, in place as they investigated.
No children aged under 5 were allowed on the train and all passengers must remain seated - and not to sit on their parents' knees.
"At this stage it is not known how long it will take to complete the investigation, which will look at a range of factors including rolling stock, infrastructure and human aspects.
Our thoughts are with the family of the young boy involved in Saturday's accident."
The family, who were not from the Coromandel, declined to comment about the incident.
A Middlemore Hospital spokeswoman said the toddler was now stable in a ward.
The Herald understands the child underwent surgery this week but was now recovering well.
When approached this week, Mr Scott and wife, Wailin, declined to comment any further of the incident as it was still under investigation by the NZTA.
Mrs Scott, who is also a general manager, heard through the 19-month-old's grandmother that he was on the road to recovery.
"We're just pleased that the child has survived."
The company had a good safety record, she said.
"We've always complied with everything that the NZTA have asked of us, so they will do what they have to do but I think they know that we run a safe operation."
Locals spoken to by the Herald felt the parents were to blame for not paying enough attention to the child and hoped the train could continue its operation.
Coromandel i-Site manager Sandra Wilson said the incident hadn't put visitors off.
"It's one of our number one tourist attractions."
Coromandel business association chairperson Brenda Kelsey believed NZTA would make the right decision and allow the company to go back to operating as normal.
"They will work it out and look at in perspective. I'm sure it will be a flash in the pan and I don't think it will do anything to Coromandel town."
She felt sorry for the staff at Driving Creek and its owner Barry Brickell who was an "icon" in the town.
