Mr Esipisu appeared to play down the economic viability of the project, saying the completion of the Naivasha-Kisumu section would influence neighbours to take on the project.
The Transport ministry says the SGR train tariffs will adequately cover the cost of the loan, operating profit and public revenue without burdening the users.
The ministry says the trains will charge as low as half of the current bus fare for a third-class ticket.
In a series of agreements reached between President Kenyatta and Chinese Prime Minister Li, Kenya also allowed the Chinese to manage the security and operations of the completed version of the SGR line between Mombasa and Nairobi.
The meeting between Mr Kenyatta and Mr Li was on the sidelines of the Belt and Road Forum, a programme by the Chinese to expand influence through trade by building infrastructure in a network of more than 60 countries in Asia, Europe and Africa.
President Kenyatta, in another meeting, met with his Chinese counterpart Xi Jinping, who will be sending a “special envoy” for the launch of SGR.
On Monday, Kenya admitted it would be unable to handle the security operations of the SGR and asked China to stand in.
The two leaders agreed to elevate the railway to “a specialised security installation” to be managed by the Chinese “until our capacity to manage operations is enhanced”.
The idea, according to Mr Esipisu, is to ensure it runs smoothly and is without incidents.
Few details were provided concerning the exact role of China, but State House said the Chinese would handle scheduling systems, monitoring of the line, installation of security surveillance and training of local staff to take up these duties after several years.
The SGR has been President Kenyatta’s pet project since he came to power.
Though criticised by some economists for creating a huge debt, President Kenyatta argued before this trip that the railway line is the first step to open up Africa to integration and expand trade.
“I don’t think it is Kenya’s railway. It belongs to Africa,” he had argued last week.