The commission was established by the Government in 2015 to advise and make recommendations to Ministers on the national minimum wage. It has an independent chairman appointed by the Government and involves trade unions, employers and campaign groups.
The Irish Congress of Trade Unions (Ictu) has pulled out because it says it cannot "in good conscience" be part of any recommendation that would fall under that threshold.
The withdrawal on Tuesday evening by Ictu raises questions about its future.
Last year, the Low Pay Commission recommended an increase of 30 cent to the minimum wage for adults, bringing the rate to €10.10 per hour. Earlier this summer, it deferred making a recommendation to the Government on a new rate for the national minimum wage until September.
It is understood there was strong disagreement between members on the issue at the time.
On Tuesday evening, the general secretary of Ictu Patricia King said: “We could not in conscience be party to any recommendation that did not afford the lowest paid workers in the Republic of Ireland an increase in excess of two per cent similar to other sectors in our economy.”
Ms King continued: “The lowest paid in our society suffered disproportionately during the last recession and we won’t be party to a process that leaves them behind.
“Therefore it is with regret, but with clarity that we can no longer be part of this Low Pay Commission. There can be no going back to the old ways where the lowest paid are left behind. We will continue to campaign through other fora for a just increase,” Ms King said.