One of the "ugliest" buildings in Brisbane would be demolished and redeveloped under an altered plan for the state government's proposed bus and train tunnel.

The $5 billion project, running from Dutton Park in Brisbane’s south to Spring Hill in the north, will help solve a bottleneck problem in the south east Queensland rail network.

An earlier model would have see an underground station next to the Roma Street Parklands in the city.

The government now wants to acquire the outdated Brisbane Transit Centre nearby and redevelop the site, with a platform to be built underneath, Premier Campbell Newman has announced.

“This we believe will save hundreds of millions of dollars and allow us to deal with a building that has been voted on many occasions as the worst eyesore of the city of Brisbane,” Mr Newman told reporters in Brisbane on Sunday.

The building’s owners had been trying to sell for some time and were asking for at least $100 million.

“We hope they’ve got a sharp pencil, we’ve got a sharp pencil too, we want to minimise the cost for tax payers,” Mr Newman said.

The changes would shorten the required tunnel distance and compress construction.

“(It is) a remarkable opportunity to get rid of one of the ugliest buildings in Brisbane and build something fresh – a much more iconic gateway for the city,” Transport Minister Scott Emerson said.

The Premier admitted the plans had been “evolving” since the Liberal National Party shelved Labor’s alternative cross river rail project.

The ongoing changes meant the project was merely a “pie in the sky dream”, Opposition Leader Annastacia Palaszczuk said.

“We need to see the full business case when it comes to this tunnel,” she said.

“We know that it is unfunded and it is uncosted.”

Labor’s cross river rail alternative was “shovel ready” and had secured a federal funding commitment, she said.