The first train on the section where the accident happened in Balasore started its journey at around 10.40 pm on Sunday, 51 hours after the horrific crash which killed 275 people, officials said.
The goods train was seen off by Railway Minister Ashwini Vaishnaw as scores of mediapersons and railway officials looked on.
The train carrying coal is headed towards Rourkela Steel plant from Vizag port and is running on the same track where the ill-fated Bangalore-Howrah train met with the tragedy on Friday.
The Howrah-bound train crashed with the capsized bogies of the Coromandel Express which had collided with a stationary freight train seconds earlier.
"Down-line restoration complete. First train movement in section," tweeted Ashwini Vaishnaw.
Barely two hours after the restoration of the downline, the upline was also restored.
An empty goods train was the first train to run on the up line of the accident affected section.
This is the same track on which the Coromandel Express was running before it entered into the loop line to crash into a stationary goods train.
"Three trains have left from the section (two down and one up) and we have planned to run around seven tonight. We have to take this entire section towards normalisation.
"Our objective is to ensure that all the missing persons' family members find them as soon as possible. Our responsibility is not over yet," said a visibly emotional Vaishnaw as he announced the restoration of the accident affected section.
Around 200 bodies so far remain unidentified.