This is despite a consultant's report recommending remedial work start in September 2016 to stop a repeat of flash flooding over rail tracks causing delays to hundreds of trains for thousands of hours in November 2014 and May 2015 at Fortitude Valley, Central and Bowen Hill stations.

The Opposition immediately questioned if some of the $67 million announced for the Central Station upgrade on Monday could be "better spent".

Both Queensland Rail and Brisbane City Council have baulked at the recommendation from Jacobs to do the work at night over between 30 and 45 weeks; or by completely closing the Fortitude Valley train station for four weeks from September 2016.

The work would create major problems in Fortitude Valley's business areas.

Consultants Jacobs in January 2016 recommended replacing water pipes around the Valley train station from September 2016 ahead of the storm season and be completed over three years.

It estimated the cost of installing bigger pipes was between $17.1 million and $19.2 million.

The report blamed drainage pipes under the station that were too small, rail tracks that were six metres lower than the rest of Fortitude Valley and one drainage pipe that was 80 per cent blocked for flash flooding over rail tracks at Fortitude Valley.

The blocked pipe was cleared quickly, but no further work has been done although electronic sensors have been installed to give Queensland Rail staff 20 minutes notice before water flows over the Valley's rail tracks.

No remedial work is planned.

Queensland Rail defended taking no action as the 2016-17 storm season approache and said it was waiting on an alternative plan from Brisbane City Council.

"The council is working on a revised plan which has the potential to further improve flood immunity," a spokeswoman said.

"Queensland Rail is now seeking further information about the relevant costs; timeframe and impact associated with the revised plan and is meeting with Council later this month to progress this."

Brisbane City Council is completing its own hydraulic engineering study into the problem to minimise "inconvenience to commuters."

"Council and Queensland Rail have agreed to seek other options for resolving flooding issues at the Fortitude Valley Station, which would minimise line closures and therefore inconvenience to commuters," their spokeswoman said.

"A hydraulic engineering investigation is being conducted to identify alternative options."

The lack of progress into another emerging major rail problem in Brisbane angered Opposition transport spokesman Andrew Powell.

Mr Powell questioned if any of the $67 million spent on upgrading Central Station could have been spent halting flash flooding.

Mr Powell called on the Premier to reveal what portion of the $67 million Central station facelift would address flooding issues.

While platforms will be raised to improve disability access, there was no mention of tackling flash flooding.

"Will any of the money go to alleviating the flood events there," Mr Powell said.

"And if not, why not?" he said.

"While rejuvenating the station is one thing, it's another entirely if trains remain unable to pass with water over the tracks," he said.

He said delays to repairs at Brisbane's flood-prone inner-city stations were another example of the Palaszczuk Government "dragging the chain" on vital infrastructure.

"Once again, this do-nothing Labor government is more intent on fighting itself than doing the hard yards and providing the investment that will get Queensland moving," he said.

Transport Minister Stirling Hinchliffe did not say if he was satisfied with the delays to replace the pipes around Fortitude Valley before the storm season.

He said it was a complex issue.

"Queensland Rail is considering the recommendations alongside Brisbane City Council, to improve flood immunity at Fortitude Valley station," he said.

"This is a complex, long-term project and expected to take at least three years to implement."

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