The minister met the prime minister after a meeting of the Cabinet and left the city soon after, his staff told PTI.
"I met the Hon'ble Prime Minister @narendramodi taking full moral responsibility," Prabhu said in a tweet. The prime minister, he added, had asked him to wait.
Prabhu, under pressure from the opposition to resign, said in a series of emotional tweets that he was "extremely pained" by the two derailments in Uttar Pradesh on August 19 and today.
"In less than three years as Minister, I have devoted my blood and sweat for the betterment of the Railways. Under leadership of PM, tried to overcome decades of neglect through systemic reforms in all areas leading to unprecedented investment and milestones," he said.
On August 19, 13 coaches of the Kalinga Utkal Express derailed in Khatauli, Uttar Pradesh, killing over 20 passengers and injuring over 150.
Today, four days later, at least 70 people were injured when the Kaifiyat Express derailed in Auraiya in the state.
Later in the day, a train collided with a lorry at an unmanned rail crossing in Villupuram, Tamil Nadu. Railway officials in Delhi described it as a "minor incident".
Prabhu, who through this week gave out information on the Utkal Express derailment and the restoration work through his official Twitter handle, had earlier taken action against eight officials, including a member of the Railway Board for the incident.
Soon after Prabhu's tweet about meeting the prime minister, the government announced the appointment of Air India CMD Ashwani Lohani as chairman of the Railway Board.
According to sources, Lohani takes over from A K Mital, who had submitted his resignation to the minister last evening. The resignation was accepted today morning.
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