The federation said on Tuesday it would give the Democratic Alliance-controlled provincial government until Thursday to
withdraw a "threat of deductions".
Failing this, it would ballot its members for "support strike action".
It was reacting to a letter from Premier Helen Zille to the provincial secretary of the National Education, Health and Allied
Workers's Union (Nehawu), dated September 2 and faxed to Nehawu on Monday.
In it, Zille said her administration had been directed by the national department of public service and administration in writing
to strictly apply the principle to striking employees.
"The [Department of Public Service and Administration] has furthermore warned that departments who do not effect the
deductions timeously will have to account for this in terms of the Public Finance Management Act," Zille said.
"This administration therefore has no option but to comply with the directive."
The Congress of SA Trade Unions (Cosatu) said in a statement on Tuesday that the DA should align itself with strike resolution procedures at national level, where the issue of deductions was "being negotiated".
The province's stand was "clearly an attempt by the DA government to victimise the workers who were on strike", Cosatu
"It also demonstrates the deep disregard that the DA has for the constitutional right to strike and for unions.
"The matters affecting the public service which gave rise to the strike are national interest and have to be dealt with
Public sector unions announced on Monday that their near month-long pay strike had been suspended pending the outcome of consultations with members and the government over the next 21 days.