Maggie Simpson, Director General at Rail Freight Group, told an online event that the proposed new zones in the Humber, Teesside and the Liverpool City Region did not have "the right capability for transport and freight in and out".
Chancellor Rishi Sunak used last week's Budget to reveal the location of eight new freeports, which have "different rules to make it easier and cheaper to do business".
They include infrastructure planning, customs and favourable duties, with companies inside the sites offered temporary tax breaks, mostly lasting five years.
A webinar organised by Transport for the North about northern freight and logistics heard the new zones would provide an opportunity for local regeneration.
But Ms Simpson, whose organisation represents rail freight in the UK, said a better low-carbon method of transporting goods across northern England was now needed to aid the Government's ambitions of rebalancing and growing the economy.
She said: "In terms of which freeport hasn't got the right capability for transport and freight in and out, the answer is all of them. From a rail point of view none of the free ports in the North of England, have got the right rail connectivity at the moment, some are better than others but overall, they don't.
"And if I cast that net wider even looking at some of the other ones further south, there are challenges on those routes, as well but there isn't that connectivity."
She said it was "absolutely imperative" that the North has the right infrastructure for freight. She added: "Right now today, it just doesn't have that in the way that we need it and it's frankly time it changed if we're going to unlock those government's ambitions, whether that's a free port, rebalancing or economic growth."
Her words were echoed by Stewart Swinburn, a Conservative councillor in North East Lincolnshire, whose patch includes the major port of Immingham.
He said the controversial HS2 high speed rail scheme would be crucial in freeing up capacity on lines currently used for passenger services so they can be used to transport goods and materials.
Coun Swinburn said: "One of the major opportunities that we need to have is to make sure that that infrastructure is in place for us to make every opportunity available to us throughout the freeport status.
"And a lot of the things that we're talking about is with HS2 and actually releasing the rail capacity that's needed for this area to make it work for all the ports that are going to be involved in the freeport status. And we have got an opportunity there for less HGV traffic, if we get the HS2 situation right."