One of Brisbane busiest train stations - Fortitude Valley - needs millions of dollars of work to prevent a repeat of flooding that stopped all trains in both 2014 and 2015.

A six month Queensland Rail investigation has blamed drainage pipes under the station that are too small, rail tracks that are six metres lower than the rest of Fortitude Valley and one drainage pipe that was 80 per cent blocked.

These three facts – plus torrential rain in November 2014 and May 2015 – combined to put 30 centimetres of water over the train tracks in November 2014, cancelling hundreds of trains for hours.

The blunt report, by consultants Jacobs, has put forward four options to fix the problem and puts the cost of repairs by widening drainage pipes at between $17.1 million and $19.2 million.