Rail unions Aslef, the TSSA, the RMT and Unite, the STUC, Friends of the Earth Scotland and other climate groups have written to Transport Secretary Fiona Hyslop.
The letter states: “The overall approach by the Government must be to make fares as affordable as possible.
“This is what will encourage and incentivise the Scottish travelling public on to trains and away from private car travel.”
Peak rail fares, they claim, is an “unfair tax on workers” and present a barrier to rail travel for many.
The group said making the pilot permanent would help on both climate change and the economy.
The letter added: “If you were to restore peak fares it would be a retrograde step that would send exactly the wrong message at the wrong time.
“We urge you to do the right thing, scrap peak fares permanently to help Scotland meet its climate targets, grow the economy sustainably and help workers by ending this unfair tax on them.”
Transport Scotland said the extension of the pilot had allowed more data to be collected on travel patterns which would “help to inform the final evaluation”.
A spokesperson said: “The Scottish Government will carefully consider the impact of the pilot and the long-term sustainability of such a proposition before committing to any further measures after June 2024.
“This trial is an exciting and unique opportunity to encourage more people to leave their cars at home and choose a safe, reliable, and green form of public transport.”