Michael Matheson has agreed to waive the operator’s performance benchmarks until June next year.
The Transport Salaried Staffs’ Association (TSSA) said the minister had given ScotRail “carte blanche to fail”.
Scottish Labour said the decision amounted to “moving the goalposts to protect a failing franchise”, but the Government said ministers could hold the operator to account within the terms of the franchise agreement.
ScotRail is required to make sure it maintains certain levels of train operating performance as part of its contract.
Mr Matheson confirmed he has agreed to a temporary waiver on compliance, despite figures published last month showing reliability on ScotRail trains over April to June at their worst level for more than two decades. Other figures also showed punctuality on train services had worsened, with ScotRail returning its worst figures for the same quarter since 2005/06.
TSSA leader Manuel Cortes said: “It’s the job of the Government to look after the needs of Scottish taxpayers and hard-working passengers by enforcing the terms of the franchise agreement ... minister Matheson should be roasted at Holyrood.”