Former champion mountain biker Lee Craigie said ScotRail’s newly-refurbished trains on the Inverness main line still only offered “bare minimum” space for bikes.
She accused the rail industry of "cultural resistance" to accommodating riders and said it needed to do far more to embrace them than just the new UK-first bike carriages due to be introduced by ScotRail on West Highland lines next year.
The five newly-acquired coaches have had most of their seats removed to provide space for up to 20 cycles and other sporting equipment, along with the first electric bike charger in a train in the UK.
Writing in her first progress report since being appointed by the Scottish Government last year, Ms Craigie said she would lobby for change.
She said: "Reliable and affordable train travel integrated with cycling, and bus travel integrated with walking and wheeling, provide a realistic alternative to single occupancy vehicles for everyday short journeys.
"But in my experience, there is cultural resistance to accommodating cyclists on some rail services with much of the newly-renovated rolling stock providing the bare minimum for bike carriage.
"This is particularly evident on the main line north to Inverness, which could serve countless communities.
"Although it is welcome that the specially-designed adventure carriages will be operational on the Oban line by summer 2021, a cultural shift is still required within rail to make people travelling with bikes, either on trains or to and from stations, feel more welcome."
Ms Craigie pledged to “advocate for adequate provision for people wishing to travel on trains with bikes and effect cultural change within rail around integrated active travel”.
Her criticisms suggest she has made only limited progress with ScotRail since describing bike storage on its Inverness trains last year as a “disaster”, which made travelling with a bike “stressful at best and impossible at worst”.
Ms Craigie said at the time: “Thankfully, ScotRail are listening and I’ve had some very encouraging conversations.”
The commissioner’s call for improvements was backed by campaigners Cycling UK.
Jim Densham, its policy and campaigns manager for Scotland, said: “It needs to be much easier for people to combine cycling with a train or bus journey, anywhere in Scotland.
"More space is needed for cycles on trains to connect communities and enable people to be active at both ends of their journey.”
ScotRail said it would make improvements “where we can”.
Head of economic development and communities James Ledgerwood said: “ScotRail recognises cyclists as an important customer group.
"We are consistently upgrading our offer to our customers who cycle to our stations or carry bikes on our services.
“We welcome the commissioner’s report and appreciate the ambitions she has for enhancing services for cyclists on Scotland’s rail network.
"We will continue to work with her and our wider cycling stakeholders to make improvements where we can.”
A Transport Scotland spokesperson said: “The commissioner’s role is vital in driving forward the active travel agenda across Scotland and strengthening links between transport policy and other areas of government such as public health, climate change and social justice.
“The Scottish Government is committed to building an Active Nation, where more people choose to walk, wheel and cycle for everyday journeys.”