Staff working Sundays and Bank Holidays will miss out on extra pay starting from April.
Wilko bosses put the cuts due to The Living Wage, introduced by Chancellor George Osborne in July 2015.
Wilko’s 18,000 staff currently receive either time and a half or double time wages when working over 39 hours a week, Sundays, Bank Holidays, nightshifts or unsociable hours.
The premiums are due to be cut in the next two months, resulting in those working nightshifts only receiving an additional £1.50 an hour.
The company has approximately 400 stores, with reports showing a fall of 1.2% in sales in the year to 31st January 2015, which subsequently sent pre-tax profits down from £27.6m to £5.5m.
In retaliation to the increase in wages due to The Living Wage, Wilko said: “Some of the increases will be offset by the removal of the majority of our current premium payments. The remaining cost will reduce profits, demonstrating our commitment to investing in team members’ pay and benefits.”
Wilko added that it will be increasing staff discount from 13% to 20%.