With the new Forth crossing being built and major improvements planned to Scotland's busiest motorway, Mr Brown said the sector was "crucial" to the economy.
But he claimed Westminster policies were holding back progress in this vital area.
Mr Brown said: "The benefits transport brings are evident, but Westminster continuing to have responsibility for key aspects of transport policy is hampering decisions and results in slower progress on vital infrastructure and transport investment here in Scotland."
He stressed that transport "makes a major contribution to Scotland's wellbeing", highlighting the Scottish Government's "capital investment commitment of £8 billion in Scotland's infrastructure over the next two years supporting around 50,000 full-time equivalent jobs across Scotland".
Despite that investment, he said more could be done if Scots voted to leave the UK in September's referendum.
Mr Brown was speaking as the Scottish Government published a blueprint for transport in an independent Scotland, drawn from policies in the White Paper.
The report highlighted Westminster's responsibility for "key aspects of transport policy", and added that UK Government spending decisions had "included a massive reduction in the capital spending available for crucial infrastructure projects" north of the border.
"Scotland's ability to support much needed infrastructure development has been hampered by decisions taken elsewhere, both in terms of overall spending limits and in the ways in which we are allowed to spend our money as a result of Treasury rules," the report said.
"This has meant slower progress on vital infrastructure and transport investment than would have been the case as an independent nation.
Speaking at the Scottish Transport Conference, Mr Brown said: "We want to turn the tide and create the opportunities to develop a fully integrated transport network.
"Independence will ensure we not only protect the powers we have to secure more investment, but extend those powers to build a coherent transport system better tailored to the needs of the people who choose to live and work in Scotland."
He highlighted the importance of transport and infrastructure work, saying: "We know transport plays a crucial part as one of the key enablers for delivering sustainable economic growth. We can see that on the ground.
"To be signed this month, the M8 motorway improvement scheme contract, with its ground-breaking and innovative financing, will support hundreds of jobs and deliver substantial economic benefits back to the economy.
"The £1.5 billion Queensferry Crossing currently under construction on the banks of the Forth will support around 1,200 jobs at its peak and return around £6 billion to the Scottish economy. And the Aberdeen Western Peripheral Route, which is due to start construction later this year, will also support local jobs and deliver £6 billion of investment to the north east over the next 30 years."
But UK Transport Secretary Patrick McLoughlin said he did "not believe that creating an unnecessary international border, where movement by road, rail, sea and air has to be controlled", was the best way forward for either Scotland or the UK.
He insisted as part of the UK, Scotland was benefitting from rail investment which was shortening journey times, arguing this was boosting the Scottish economy by some £3 billion.
The UK Government minister said: "If Scotland is to flourish in the future, it needs to be an outward facing nation - a country that welcomes people and investment from abroad, that builds strong connections with international partners and that's wired into the global economy.
"But where we differ from the pro-independence lobby is that we believe Scotland has a better chance of achieving those goals if it's part of the United Kingdom, part of a bigger, more powerful block in which people and goods can all move freely, unconstrained by international borders where devolved administrations work alongside the Westminster Government on a shared vision to improve transport throughout the UK."
He added: "Together, we've become one of the fastest growing economies in the Western world. Together, we are modernising the UK's transport infrastructure, reversing decades of underinvestment, linking up the country to secure long-term growth, and rebalance our economy.
"I don't believe that creating an unnecessary international border, where movement by road, rail, sea and air has to be controlled, is the best way forward for Scotland or the UK.
"We have a fantastic opportunity here to put the difficulties of the past behind us and build a better future."