Speaking ahead of a rail conference in Liverpool on Thursday, Mr Brown warned the West Coast Main Line, which carries passenger trains between London and Glasgow, would not be able to cope with the predicted increase in high-speed services by 2033.
Under UK Government plans, a £32.7 billion network of new railway lines would be built in two phases, from London to Birmingham in 2026 and onwards in a "Y" shape to Leeds and Manchester by 2033. Services would continue north to Scotland on existing track, but only at half the 250mph speeds they would be capable of on the dedicated high-speed route.
The Herald revealed in March that the plans could create a choke point north of Manchester, limiting the number of freight and passenger services that could transfer on to the West Coast line, according to a planning document written by track owner Network Rail.
However, Mr Brown's analysis goes significantly further, suggesting a "double spend" would be required if a high-speed rail route is not built all the way to Scotland early on.
"If the UK Government goes just as far as Manchester and that's left unattended to, you then have to look quite separately at how you improve the capacity of the West Coast Main Line, which is going to cost multi-billion pounds' worth of investment," Mr Brown said.
"And if you do that separately from high-speed rail and, say in 10 years' time, you have high- speed rail all the way to Scotland, it's a further tranche of investment. It's double spending really."
He added: "In my mind it's better to do it as a whole right the way through, because high- speed rail gives you that capacity for freight and passenger (services) right from the start."
The consequence of the existing plans would be a negative impact on freight and passenger services to Scotland, Mr Brown added.
"It means that building high- speed rail to Manchester actually works to the disadvantage of Scotland. You've got a choke point created whereby you're going to have to start saying no to freight, it's going to have to start finding other modes; and also to passengers as well." His comments, which are expected to be echoed by Infrastructure Secretary Alex Neil when he shares a platform with UK Transport Secretary Justine Greening on Thursday, are the latest sign of the Scottish Government's commitment to a London to Scotland high-speed rail network, which it estimates to be worth £20bn to the Scottish economy.
Its stance has been welcomed by business leaders, although critics have pointed out that it is not yet clear where the £26bn required to extend a link from Manchester to Glasgow and Edinburgh would be found. A clearer idea of exact costs and route options is expected to be published later this year, and the SNP has committed to setting out a timeline for building the route by 2016.
A spokeswoman for the Department for Transport said it was continuing to have discussions with the Scottish Government about its high-speed rail plans. She said: "The Coalition agreement makes it clear that our vision is for a genuinely national network with high-speed services from London to the Midlands and the north, including Scotland. We see phases 1 and 2 of the High Speed 2 project as the best way to make progress towards that goal."
"We are in discussion with the Scottish Government about their aspirations for high-speed rail. It is imperative that the process we are developing is as thorough and rigorous as possible so that we end up with the best value solution, whether that be a full high-speed solution, upgrades to existing infrastructure to remove bottlenecks, or a combination of the two."