The penalties follow a weekend of bank holiday travel chaos that saw Glasgow Central station closed because of problems with overhead wires.
ScotRail, run by Dutch operator Abellio, missed performance targets in 22 out of 34 areas in the first three months of 2018, according to the latest official figures. This resulted in £1.6m of fines –nearly £400,000 more than in the previous three months.
The firm insists it has now identified ten priority areas and has developed detailed plans to address the key issues which caused the problems.
But opposition leaders branded the figures “shocking”.
“ScotRail has left passengers having to pay a small fortune for delayed and overcrowded trains,” said Labour’s rural affairs and connectivity spokesman Colin Smyth.
“And even when trains are not cancelled, they still can’t be guaranteed to stop at the stations they are supposed to.
“The fact that ScotRail seems to think this performance is acceptable because the fines are put back into the industry shows real contempt for the impact these missed targets have on passengers. This is simply unacceptable.”
ScotRail’s performance through quarterly figures called the Service Quality Incentive Regime (Squire). A range of areas including station CCTV, litter and contamination, train seats, refreshments, food, help points, telephones, ticket machines, train and station toilets, cleanliness, taxi ranks and car parks fell short of the mark in the most recent figures.
A spokesman for ScotRail said there has already been improvements in on-train ticket inspections and booking office opening times.
“We have developed detailed plans to keep improving the high level of service our customers quite rightly expect,” he added.
ScotRail also said that the £1.6m financial penalties are not fines, because the money goes into a reinvestment fund used to enhance Scotland’s railway.
The operator has also faced repeated criticism over the controversial practice of “stop skipping” where trains simply fail to stop at stations. Mr Yousaf has branded this “simply not good enough” when it emerged in January that 20 trains a day were doing this.
A Transport Scotland spokesman said the Squire regime is the “toughest of its kind” in the UK and is at the heart of efforts to improve the rail service.
He added: “This level of penalties is disappointing, especially in comparison to the corresponding quarter in 2016/17.
“We have robustly challenged ScotRail on the issues which are contributing towards, not only the Squire performance but the non-delivery of the fundamental expectation of staffed stations and trains.
“As a result ScotRail has committed to two reviews, one on staffing/recruitment and the other to produce a recovery plan to focus on more effective methods to resolve and repair faults.
“All penalties accrued are reinvested in the franchise through improvements to the Scottish Rail Network.”
Glasgow Central’s high level was closed completely at 10:45pm on Saturday after ten trains travelling on high level routes lost power at around 9:15pm.
Passengers stranded on affected services were helped off trains by staff, with all customers off the trains by 12:45am on Sunday. Disruption continued into Sunday afternoon. Train lines re-opened at 1pm but ScotRail said some routes were winding down early to allow for essential repairs to be carried out.
A ScotRail Alliance spokesman said: “We apologise to anyone affected by the disruption caused by severe damage to the overhead wires at Glasgow Central.”
The firm is investigating what may have caused the disruption to the overhead wires.
Meanwhile Glasgow Queen Street was named Britain’s most unpopular railway station in a survey of passengers.
Independent watchdog Transport Focus took the views of 28,000 people.