Transport minister Humza Yousaf has said that ScotRail could do better but insisted the rail operator's performance is not "apocalyptic".
Mr Yousaf, who has come under fire for problems on the railways, told MSPs he was "disappointed" with new figures showing passenger satisfaction had fallen.
He said the research for the national rail passenger survey (NRPS) had been carried out before an improvement plan for ScotRail had started to take effect.
A total of 86 of the 270 measures outlined in that have already been completed, the minister said, with work being under way on the "vast majority" of those that still remain.
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He thanked rail workers, saying that "because of their direct efforts we have seen an improvement in performance across the railway network in Scotland".
Mr Yousaf said: "Let me be clear: ScotRail is not yet performing at the level I would like it to.
"However, let's also be equally clear, neither is the situation the apocalyptic scenario often painted by our opponents."
He pointed to a 6% improvement in the most recent performance statistics - adding these had been delivered at a time when Scotland had been hit by "high winds, including two storms".
In the same period, 0.59% of train journeys were affected by stop skipping - a practice where trains do not stop at all stations - with the minister citing this as "further proof that the improvement plan that I instructed is working".
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He added he was "confident that continued focus from staff and management" would see performance improve to a level that "passengers are entitled to expect".
He also insisted some of the cash for £3 million Scottish Government scheme to give season ticket holders one week of free travel would come from a fund ScotRail controls.
MSPs had previously been told the Service Quality Incentive Regime (Squire) railway improvement fund, which is built up through penalties imposed for delays, had been earmarked for ''other initiatives''.
Phil Verster, who is stepping down as Abellio ScotRail managing director to take another job in the industry, told a committee he "can't vouch for whether the scheme goes ahead or not".
Mr Yousaf told Parliament the fund, which currently stands at £2.6 million, would be used, with a deduction of £1.8 million for the Scottish Government's fares initiative.
"The remaining £1.2 million to fund the initiative will come from the Transport Scotland budget," the minister added.
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Conservative MSP Liam Kerr said the relationship with the Scottish Government appeared to have "driven Mr Verster from his post".
He said: "Ill-thought through announcements regarding public-sector bids and the future of the franchise, uncosted raids on the Squire fund without adequate consultation for which Mr Verster cannot vouch, whilst the situation on the ground deteriorates for the travelling public with customer satisfaction down and the latest performance data showing average annual punctuality lower than the contractual target.
"It is not good enough, so can we have assurances from the transport minister that Mr Hynes will have the full support of this government, that the minister will cease to bounce policy into the public domain without proper consultation with either ScotRail and/or the various stakeholders and will he promise those passengers so fed-up with the performance of our railway network that he will stop with the gimmicks and the policy making on the hoof, and finally focus on resolving the under-performance of our national railway?"
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Labour MSP Neil Bibby said: "Passengers are fed-up with the level of delays, cancellations, overcrowding and skip stopping.
"Despite everything the minister has said, today's passenger survey by Transport Focus confirms that passenger satisfaction is at a 14-year low.
"On almost every single measure, satisfaction is down compared with the previous year. Only 38% of people are satisfied with the way ScotRail deals with delays.
"The reality is targets continue to be missed, passenger confidence has slumped and the ScotRail chief has announced he's leaving after just 18 months.
"The minister agreed an improvement plan with ScotRail.
"In October he told Parliament he expected ScotRail to hit the 91.3% performance target by the end of March."
Mr Bibby called on Mr Yousaf to take responsibility if the deadline was missed.
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Mike Rumbles MSP, for the Liberal Democrats, said: "Phil Verster made it clear to the Rural Economy Committee just before he resigned that he had not agreed, that is not agreed, to the transport minister's attempted raid of £1.8 million from the service quality regime fund to help fund the government's free week of travel.
"This fund can be used for disabled access in stations. My constituents in the north-east have had access turned down to Insch station because they are told there is not enough money.
"How can the minister say in his statement that disabled access at stations like Insch will not be impacted upon by this attempted financial raid for a week's free travel?"
Greens co-convener Patrick Harvie called for clarity on whether a public-sector operator for the railways would have to bid competitively against private companies.
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