ScotRail has been fined £483,000 for failing to meet required standards for trains and stations.
Performance inspectors found areas which missed targets included station toilets, ticket machines, train seats, toilets and cleanliness.
The results follow criticism of the ScotRail Alliance franchise, operated by Dutch firm Abellio, for delayed, cancelled and over-crowded trains.
ScotRail said the figures showed they "can never stop striving to improve".
Earlier this month, a petition to strip Abellio of the ScotRail contract was given to Transport Minister Humza Yousaf.
Following the release of the latest figures, which cover the period between July and September, Mr Yousaf said: "The latest quarter two results show a combined penalty of £483,000, and penalties to date for ScotRail's performance currently stands at £2.2m.
"This indicates further improvements can, and will, be made in terms of aspects of service delivery such as improvements in station shelters, train doors, train toilets and train announcements.
"As such, Transport Scotland have requested remedial action plans from ScotRail to focus on improving the performance in these areas."
Phil Verster, managing director of the ScotRail Alliance, said the operator had signed up to an even tougher inspection scheme than in previous years.
He said: "We did this because we know that being part of a tough scheme will mean that our staff will always be focused on delivering the best possible service to our customers.
"These figures show that, even although we are delivering in lots of areas, we can never stop striving to improve even further."
He added: "We have announced our largest-ever train improvement plan.
"Over the course of the next few years we will be spending £475m on new and refurbished trains as well as great services like enhanced wi-fi and at-seat power sockets."
ScotRail Alliance has previously published details of how it hopes to improve performance on the network.
The plan includes the protection of "golden trains", services that have the biggest impact on the network if they are delayed or cancelled.
First Minister Nicola Sturgeon has said she is "absolutely committed" to fixing the problems on Scotland's railways.
She said it was "absolutely incumbent" on operator Abellio to deliver services that met those expectations.