Edwina Hart accused UK officials of "ignorance" amid suggestions passengers could have to change trains on some services between Wales and England.
Responsibility for the Wales and Border network will be devolved in 2017.
A Department of Transport spokesman said no decisions would be made without considering local views.
Services from Aberystwyth to Birmingham and Milford Haven to Manchester via Cardiff, are among routes which could be affected.
In last year's St David's Day agreement, the UK government wrote: "In order for the secretary of state for transport to ensure proper accountability, it is likely that services primarily serving English markets will be placed into other franchises for which the Secretary of State for Transport is the franchising authority".
Responding to suggestions some passengers may have to change trains on cross-border routes, Mrs Hart said some Whitehall officials "don't actually understand how things work and what are important".
"I base some of their comments on ignorance rather than a conspiracy theory," she said.
"We want to ensure those services remain within the franchise."
John Rogers from campaign group Railfutures Wales said: "It's ludicrous, it's impractical, it's being done behind the scenes with a lot of secrecy initially and we're determined to fight it".
"It's not in the interests of passengers.  People hate changing trains, it's a deterrent and it would affect the tourist industry," he added.
A Department for Transport spokesman said: "We are working closely with the Welsh government to develop plans for cross-border routes and stations as we move towards devolving the next Wales and Border franchise".

Some 1,500 officers have been deployed to the Olympic Stadium area, authorities have said.
Officials are in high alert following Tuesday's attacks in Brussels.
Last year, a friendly between Germany and the Netherlands in Hannover was called off two hours before its start due to a security threat, four days after the Paris attacks.
One of the targets in Paris was the Stade de France, where Germany were playing France in a friendly match.
Some 72,000 people are expected to attend Saturday's match in Berlin between two of the favourites for June's Euro 2016.
In the hours ahead of the game, fans gathered around the stadium amid a heavy security presence.
They face security checks and bag searches before entering the arena.
"This is of course a very large event drawing lots of people. Like all large events, there is a certain risk involved, so we are well prepared," Berlin police spokesman Stefan Redlich told Reuters news agency.
"We searched the Olympic stadium with dogs trained to sniff out explosives before we let the fans in. So we can be relatively certain that there are no dangerous objects in the stadium."

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14 January 2015 Last updated at 18:28 GMT
The carriage has spent four months at Locomotion, the National Railway Museum in Shildon.
It took the World War Two prime minister's coffin from London to Oxfordshire in 1965.
The restoration cost about Â£30,000.
Look North's Ian Reeve reports.

Staffordshire Police said officers were called at 03:55 BST to the southbound carriageway, between junction 16 for Crewe/Stoke-on-Trent and 15 for Stoke-on-Trent.
The man was taken to hospital where he remains in a critical condition.
The southbound stretch was closed after the crash and reopened at about 10:00. Motorists were warned of delays during the morning.
See more updates on this story and others from across Staffordshire and Cheshire here
West Midlands Ambulance Service said the man, believed to be in his 20s, was lying on the hard shoulder when crews arrived.
Spokesman Jamie Arrowsmith said: "He had suffered multiple serious injuries and was suffering from a reduced level of consciousness.
"The man received specialist trauma care at the scene before being anaesthetised in order to stabilise his condition.
"He was then transported to Royal Stoke University Hospital on blue lights and sirens for further emergency treatment."
Claims direct cross-border rail services could be under threat due to devolution have been dismissed by Wales' transport minister.
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Security is tight in the German capital, Berlin, Germany host England in a friendly football match.
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A railway carriage that carried Sir Winston Churchill's coffin to his final resting place has been restored in County Durham.
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A stretch of the M6 was closed after a pedestrian was hit by a lorry.