Indian Railways was suffering because of neglect over several years and lack of investment in infrastructure development, the minister said.
"In the last several years we have not invested as much as should have been invested," Prabhu said at the Eastern Railway headquarter here.
"Because of neglect over several years, Railways is suffering," he said.
The minister said that steps were being taken to rectify these, but this would take some time before results were visible.
"You cannot increase the number of trains or rolling stock with the given infrastructure," he said.
Illustrating the present state of Indian Railway, Prabhu said an ICU patient cannot be expected to join a marathon race against the Chinese railway now.
"A marathon cannot be done by an ICU patient and today's Indian Railway cannot be compared tomorrow with Chinese railway. We must first understand where railway was and in that context we must compare today's railway with any other railway," Prabhu said earlier at a Bharat Chamber of Commerce session.
Emphasising that the government needs time to make up for the past, he said, "We are starting to run from zero point and still want to win the race" adding that in the next five years the government was investing 120 billion USD in the railways.
"Many of the problems that we face today is because of the lack of investment in the past and also because modernisation has not been initiated in the railways," Prabhu said.
He said that Indian Railway is always compared with that of China but to reach that stage India must make investments.
Prabhu during the day also inaugurated a mobile-based application system introduced by Eastern Railway, R-Mitra, to ensure women's safety and said that it is an "extremely useful app" that could be used by regional railways nation-wide.