At least 20 people died as the train ran over them as Dhamara station near Saharasa in Bihar.
The CBI also said no conversation happened between Bansal and his nephew Vijay Singla which can be connected to the case.
Earlier in the day, a Delhi court took cognisance of the chargesheet the CBI had filed in the case on May 2.
According to sources, Rahul Bhandari along with railway contractor Sandeep Goel received Rs 14 lakh bribe for the top posts.
CBI sources said that Pawan Kumar Bansal was being questioned as a witness and this might change if his role was found to be suspicious.
Sources added that Bansal must have been aware of the favours given by his nephew Vijay Singla.
The RPF Association has been illegally occupying four properties including one in Delhi.
Vivek Sahai reportedly held additional charge as Member, Traffic, during Mamata Banerjee's tenure and another eligible candidate was denied the post.
The CBI had sought files from the Railways on transfers spanning tenures of Mamata Banerjee to Pawan Kumar Bansal.
Illegal land dealings and Bansal's links with an association that the MHA had recommended a ban against could trouble him in the near future.
Sources say Bansal quit after the CBI got evidence that suspended Railway Board member Mahesh Kumar had met him.
Pawan Kumar Bansal on Friday resigned as Railway Minister.
Pawan Kumar Bansal resigned as Railway Minister on Friday.
"Pawan Bansal case is a very shameful case, but case of Ashwani Kumar is also not very small," he said.
The Railway Minister had stopped attending office after reports came of his involvement in the cash for jobs scam in the Indian Railways.
CBI sources say the Railway bribery case is turning out to be a multi-crore scam with roots deeper than what meets the eye. The question is what action did the agency take when it was aware of a similar recruitment scam reported by CNN-IBN in 2010.
Railway Minister Pawan Kumar Bansal's nephew has been arrested on charges of receiving bribes from a railway official for promotion.
Prime Minister Manmohan Singh is still not keen on Law Minister Ashwani Kumar's exit, sources said on Thursday.
Law Minister Ashwani Kumar, who was earlier denied a meeting with the PM, however, was present at the meet.
The investigative agency sought clarification on the basis of some phone conversations tapped by them.
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