The body recommended the Scottish Government should have the power to permit new foot crossings, such as in areas where there are none for miles around.
However, Network Rail, which runs tracks, vowed to fight the plans, which would also include permitting walkers to use private crossings, such as those currently restricted to farmers.
The firm has clashed with groups such as Ramblers Scotland, which accused it of eroding access rights by closing dozens of such crossings.
British Transport Police has caught increasing numbers of walkers taking illegal shortcuts across tracks, including nearly 90 in the Perth and Inverness areas last year.
The commission said people’s access rights to land either side of railways in Scotland under right-to-roam legislation were being “frustrated” by the lack of public level crossings.
It said: “The distance between crossings available for use by the public is often considerable.
“This may encourage people who are exercising access rights to cross the track where it is convenient for them to do so, even though there is no crossing.
“We take the view that safety is more likely to be improved if members of the public are able to use a crossing rather than continuing to cross the track at unprotected locations, and contrary to the statutory prohibition on trespass on the railway.”
However, the commission added: “Scottish ministers must be satisfied that such a crossing is ‘necessary for the enjoyment of access rights generally in the local area’.”
Network Rail told the commission a new foot crossing would cost £10,000-13,000. A footbridge would cost £1.1 million.
Ramblers Scotland said it was significant the report recognised that in many parts of Scotland, “public access is taken informally across railway lines where hillwalkers and others do not have practical access to more formal crossing points”.
Director Dave Morris said: “We expect the rail operators to respect the existing basis by which pedestrian public access is taken across railway lines in Scotland, by level crossings or more informal means.”
He also called for action in Glen Lochy, on the Glasgow-Oban line, where hillwalkers regularly cross the tracks because the official route via a culvert means bending double.
Network Rail said it was determined to close level crossings rather than open new ones. A spokesman said: “We would not wish to see any new crossings. Misuse of level crossings is the single biggest risk to rail safety. We would not contemplate allowing level crossings if we were building the railway now.
“We believe closing crossings and diverting rights of way off the tracks offers the best solution to improving safety.”
A Transport Scotland spokeswoman said: “Railway safety policy is reserved to the UK government. However, the Scottish Government will input to the UK government’s consideration of the recommendations.”