Newport’s new station opened in September 2010 ahead of the Ryder Cup golf tournament at nearby Celtic Manor.
But this month passengers reported dodging puddles on walkways.
Network Rail said “interface issues” with the roof’s construction material were being addressed and contractors said two leaks were remaining.
The new roof is comprised of 31 air-filled cushions, made from the polymer ethylene tetrafluoroethylene, which give a “bubble-wrap” effect.
The cushions are created using two layers of film measuring around two to three strands of hair in thickness.
The panels for the Eden Project in Cornwall are also made of the material.
Councillor Matthew Evans who was the leader of Newport council when the station revamp was unveiled has described the leaks as “embarrassing”.
Evans told the BBC: “You will have snagging problems with any new building but when you’ve still got problems three years later it doesn’t exactly fill you with confidence.
“I don’t have anything against the design – I called it thought-provoking at the time – but it needs to be practical.
“The roof has had problems for some considerable time. It is embarrassing.
When it was unveiled, Network Rail called it a distinctive station “that is cost-effective to build and maintain, eco-friendly and fit for the 21st Century and beyond”.
A Network Rail spokesman said: “We still have verification works to complete before we are happy that the roof is leak free.
“The station represented a £20m investment when it was redeveloped in 2009.
“The station reopened in time for the 2010 Ryder Cup golf competition in Wales.
“Since then, we became aware of interface issues between some of the materials used in its construction.
“We agreed a remediation plan with our contractor and we are delighted that the works are now complete.”
A spokesman for Galliford Try said: “We have rectified the readily accessible leaks identified in the roof with the exception of two which require possession of the line.
“We will attend to these at the first opportunity.”
Arriva Trains Wales said the matter was an issue for Network Rail and its contractor.
A spokeswoman added: “We’re keen to resolve any issues as soon as possible for the benefit of our passengers.”