"It's clear that accessibility has been an afterthought in developing transport services," said Local Transport Minister Simon Lightwood.
The report found nearly seven in 10 disabled people and those travelling with them experienced barriers to travel either most or all of the time.
Last summer, LNER apologised to Baroness Tanni Grey-Thompson after she was forced to "crawl off" a train arriving at London's King's Cross.
The 11-time Paralympic gold medallist told the accessible transport inquiry: "In my lifetime, I will not be able to get on a train without the permission or support of a non-disabled person."