"Big delays, drawn-out travel times and the number of cancellations could speak to bad management from the state," Monica Rupprecht Hjort at the auditor's office told the Dagens Nyheter newspaper.
The auditors also said that blaming the weather was not acceptable.
Meanwhile, the blame game reached parliament on Thursday during a budget debate, with the government and the opposition at loggerheads over who had the responsibility for the erratic national train system.
Social Democrat MP Anders Ygeman told the Riksdag on Thursday that the infrastructure minister, the Transport Authority, and SJ itself had promised in the autumn that this winter would prove a smother ride for passengers than previous winters.
"And here we are again, the snow has arrived and the trains stand still," Ygeman said as he addressed the parliamentary floor.
He, however, immediately faced a barrage of criticism by his Moderate Party opponent Jan Evert Rådhström who said Ygeman was riding on the back of the blizzard to score political points.
"My criticism is that a week has passed since the heavy snowfall but snow still covers the tracks," Ygeman responded.
The government has added 8.2 million kronor ($1.2 million) to the railway maintenance budget in 2013.