Professors Katy Hayward and Nicola McEwen said "specialised facilities", such as pens for inspecting live animals, would be needed at sites where physical customs checks are carried out.
It comes after First Minister Nicola Sturgeon launched a new paper setting out her updated economic case for independence.
The document said an independent Scotland would apply to re-join the EU and the Scottish Government "would put in place measures to smooth any checks required as a result of Brexit on goods moving to and from England and Wales".
It said physical customs checks "would likely only be undertaken on the two main trunk routes between England and Scotland or at rail freight terminals". Answering questions from journalists, Ms Sturgeon confirmed these trunk roads would be the A1 and A74(M), which becomes the M74.
However, there are around two dozen other cross-border roads.
In a report published earlier this year, Prof Hayward, of Queen's University Belfast, and Prof McEwen, of the University of Edinburgh, examined the issue of Scotland's border after independence.
They said "for the most part, it can be expected that the main trunk roads would be designated for customs movements, including with some form of border control and inspection facilities, whilst the minor routes could be monitored by other means, including cameras".
The experts told The Scotsman that physical checks would primarily relate to sanitary and phytosanitary products, which involve animal and plant health, biosecurity and food standards.
Specialised facilities would be required for these checks, for example "border control posts, with refrigerated facilities for checking chilled products, or pens for inspecting live animals".
"Those products subject to checks (and in the absence of a veterinary agreement UK-EU, there will have to be 100 per cent checks on certain products) will have to pass through those two main routes," the academics said.
"With respect to the other routes, not having the infrastructure for physical checks at the border does not mean that there are no controls at all on goods crossing at those points – i.e. some could be manned/have barriers to crossing, and declarations on goods will have to be made to pass through them, unless they are being moved by trusted traders.
"Decisions to inspect some goods based on intelligence or risk assessments could be made, e.g. to combat the smuggling of counterfeit goods. Such inspections could happen away from the border.
"Checks for compliance with product regulations could also take place away from the border, e.g. in warehouses.
"But the greater the degree of divergence between both sides of the border on such regulations, the greater the risks associated with allowing such products to cross the border without inspection."
The experts added: "One of the ironies of independence is that, to manage risks and prevent smuggling, there would have to be much more co-operation between governments, transport bodies, security and other agencies on either side of the border than we see within the Union."
Speaking at a press conference on Monday, Ms Sturgeon admitted "arrangements" would need to be put in place for the transport of goods, but insisted checks "can be done in a way that doesn't disrupt trade".