KiwiRail posted a loss of $187 million last financial year - if subsidies by central and local government are taken out of the picture.
The company has tabled its annual report in Parliament, revealing it's had a difficult period.
With the money it receives from central and local government taken into account, Kiwirail made a surplus of $239 million.
However, the Government has said it wants to contribute less in future. It currently provides a subsidy of $90 million per year.
Last month it was forecast the company would have a deficit of $306 million in three years.
Chief executive Jim Quinn says freight volumes were down 13% and the number of Interislander passengers was also down.
He says it was a tough year but there had been some positives, such as increases in urban rail passengers.
KiwiRail was re-purchased by the Labour Government, which paid $690 million in July 2008. Treasury said in November 2008 that its value was $448 million.