The official said the death toll has gone up to 21, but did not give details of whether more bodies were recovered or those killed were from the injured who succumbed.
The traffic was restored completely at 4.30am on the Konkan Railway Corporation Limited (KRCL) route.
"The traffic has resumed and all the trains are running on time except for those which were diverted after the accident," KRCL's Public Relation Manager Baban Ghatge told PTI.
Five trains had to be cancelled after the accident on Sunday, he said.
"The traffic is normal now. The trains will be on time," he added.
The KRCL route terminates at Roha.
Following the mishap, services on Konkan Railway route were suspended. Some trains were diverted via Panvel-Lonavala-Pune-Miraj-Londa-Madgaon and a few cancelled.
A goods train had derailed last month on the route, affecting services.
The Railways ordered an inquiry and railway minister Mallikarjun Kharge had announced an ex-gratia of Rs. two lakh for the next of the kin those killed in the accident, Rs. 50,000 for the grievously hurt and Rs. 10,000 for passengers who suffered minor injuries.
Railway board chairman Arunendra Kumar had said that Commissioner (safety) Chetan Bakshi was conducting an inquiry into one of the worst train mishaps in the state in recent times.