Emergency services were called to the scene close to Knockmore industrial estate at about 06:45 GMT on Thursday.
No one was hurt. The train was evacuated and passengers were transferred to buses.
Translink and the Health and Safety Executive have begun investigations and the line will remain closed all day.
The transport firm's spokeswoman said: "We would hope to be in a position to resume a full train service from tomorrow [Friday] morning."
On Thursday afternoon, rail passengers were advised that a bus substitution will operate between Moira and Lisbun until 18:30 GMT to "accommodate peak time commuter traffic".
After the rush hour, a bus substitution will operate between Portadown and Lisburn and cross-border passengers will be bussed between Belfast and Newry for the rest of the day.
Translink's statement added: "Safety is our top priority and an investigation is currently ongoing.
"We are now taking steps to get the line cleared; our engineers have been on site and will be working throughout the night in order to get services back to normal for our customers."
The firm said it will be working with the Rail Accident Investigation Branch and the Police Service of Northern Ireland (PSNI) during the investigations.
Translink has apologised to their customers for the inconvenience.
The Knockmore Road, which was closed between the Moira Road and Ballinderry Road, has now reopened.
A train hit a piece of construction equipment on the railway line near Lisburn, County Antrim, a Translink spokesperson has said.