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.

On a green surface and in damp, overcast conditions, Australia fell to 8-4 and 17-5 after losing the toss.
Vernon Philander took 5-21, Kyle Abbott 3-41 and though Steve Smith ended 48 not out, Australia slumped to their lowest home total against the Proteas.
South Africa reached 171-5 by the close for a lead of 86 - Hashim Amla hitting 47, while Mitchell Starc has 3-49.
The tourists, without injured skipper AB de Villiers and pace spearhead Dale Steyn, already lead the three-Test series 1-0.
This Test is the first time since both made their debuts against England in December 2004 that South Africa have played without either of them.
In the absence of Steyn, Philander tore through the Australia top order, starting with David Warner edging a drive to a delivery so wide he could barely reach it.
Joe Burns was lbw to Abbott and, after Usman Khawaja and Adam Voges edged behind the wicket, debutant Callum Ferguson was run out by a direct hit from substitute fielder Dane Vilas for three.
From five wickets down, Australia needed captain Smith to get past their lowest home total of 58, but they were still shot out for the worst score in a Hobart Test.
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A train hit a piece of construction equipment on the railway line near Lisburn, County Antrim, a Translink spokesperson has said.
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Australia were bowled out for only 85 on the first day of the second Test against South Africa at Hobart.