Train services are back in public hands for the first time in 25 years after Dutch firm Abellio had its franchise ended three years early amid criticism over its performance.
Transport minister Jenny Gilruth said fares in Scotland are around 20 per cent cheaper than they are in the rest of the UK.
But she told the BBC's Sunday Show: "I think one of the things that passengers might expect us to do as a Government under public ownership is to reconsider the affordability of travel on rail, particularly in light of increases to the cost of living, for example.
"So it's absolutely not something that we're ruling out going forward."
Fares between Edinburgh and Glasgow are £425.50 a month, while Kirkcaldy to Edinburgh is £247.30 a month.
Scottish Conservative transport spokesman Graham Simpson said Ms Gilruth "needs to look at lowering fares so that they are more affordable".
He told the BBC: "We need a simpler fare system and also we need that smartcard that we've been talking about for years that they managed to give to COP26 delegates, but what about the rest of us?"
Delegates to the COP26 climate conference in Glasgow were provided with a free travel smartcard allowing them to travel on buses, trains and trams.
He said: "What we now do with it, though, is the important part.
"We've had the PR of it. What people now want to see is cheaper rail, trains to come on time, more services available.
"At the moment what we're seeing is rail fares going up ... we're seeing ticket offices closing or reducing their hours, we're seeing routes cut.
"That's not a better service for people across Scotland. That's a worse service.
"If you get better services, services that come on time, more options with your services and lower fares, you will get more people on to the railways.
"That will increase your income and pay for many of the changes people expect to see on our railways."