Compensation paid to travellers on the Caledonian Sleeper reached almost £1 million in less than a year.
The Scottish Conservatives have accused the Scottish Government of "running Scotland's rail services into the ground".
The figures obtained by the party through freedom of information (FOI) showed that £965,672 was paid out to passengers hit by delays between April 24 2023 and April 5 2024.
However, Transport Scotland has said the figures represent a "very small proportion" of all journeys made in the same period.
The Caledonian Sleeper was brought back into public ownership by the Scottish Government on June 25 2023, meaning the vast majority of the figure quoted covers the post-nationalisation.
It followed the re-nationalisation of ScotRail for the first time in 25 years.
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A breakdown of the figures showed that almost £700,000 of the bill went on compensation to passengers who had been delayed for more than one hour.
A total of £690,068.90 was paid in compensation to those hit by delays of an hour or longer.
Meanwhile, £163,430.44 in compensation was paid for those experiencing delays of 30 minutes.
The Caledonian Sleeper also paid out £112,172.73 in compensation for manual delay repay in the same time period.
Sue Webber, transport spokeswoman for the Scottish Tories, said: "The SNP promised nationalising our sleeper service was the best option – and yet passengers are being let down by a service that’s too often late and taxpayers are picking up the tab for compensating them.
“As with their botched ScotRail nationalisation, it appears the SNP are making a mess of running the Caledonian Sleeper.
“Shelling out almost £1million on reimbursing travellers is the last thing we can afford at a time when the SNP’s financial mismanagement is leading to swingeing public spending cuts.
“Rail users have consistently been let down by the SNP failing to deliver on their promises, and it is driving people back into their cars and onto the roads.
“If the SNP insist on nationalising Scotland’s rail services, they must make sure they’re able to efficiently run them – instead of running them into the ground.”
Transport Scotland said in the year to September 2024, less than 3% of all services were cancelled.
A spokeswoman said: “The number of compensation cases paid out across the dates discussed represents a very small proportion of all journeys made in the same period."
She said: "Any disruption to passengers is regrettable and it is only right that Caledonian Sleeper do all they can to compensate where journeys are delayed or cancelled.
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“Rather than make misinformed comments about past disruption - particularly when more than 50% of this was caused by external factors - we are focused on ensuring the publicly owned Caledonian Sleeper is a success.”
It is understood that in some circumstances compensation is paid by the Caledonian Sleeper when the disruption is caused by external factors.
Kathryn Darbandi, managing director of Caledonian Sleeper said: “Caledonian Sleeper’s performance is above average and has been improving year on year.
"That said, we want to see compensation payments reduce and we are constantly working to mitigate delays wherever possible. However, the rail network is complex and factors beyond our control have contributed to the overall compensation value.
“Our commitment to providing excellent customer service includes our Delay Repay scheme, which is a commitment provided by all rail operators."
The Scottish Government brought the service back into public ownership in an attempt to build on the Caledonian Sleeper's increasing passenger numbers.
The move to nationalise the rail franchise was welcomed by trade union bosses and saw previous operator outsourcing firm Serco's contract terminated seven years early.
Serco's £800m agreement had been due to run until 2030, before the firm attempted to renegotiate its contract.
The sleeper service runs overnight trains between Scotland and London as has been operating in various forms since 1873.
RMT union general secretary Mick Lynch described the nationalisation as a long-awaited opportunity for a national conversation on rail.
"At the heart of this must be investment in expanding and improving services, ruling out cuts to ticket offices and properly staffing Scotland’s railway to make it accessible for all," he said at the time.
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