According to documents obtained by ABC11, Town Clerk Debra Godwin got a 29 percent raise this fiscal year and Public Works Director Lenny Branch was given a 17 percent hike.
About two dozen other employees saw much smaller salary increases.
The documents show Williams had no cost of living or merit based raises in his budget approved by the Smithfield Town Council.
Contacted by ABC11 Thursday, Williams said he did not authorize the pay raises and said he encouraged the town council to have an internal audit done to clear his name. He said he had no idea who authorized the raises.
All told, the increases cost the town more than $100,000 at the same time it was cutting back on funding for some social service programs.
Town officials say Williams is still employed and drawing a salary.
"We just want to make sure that all line items are within the guidelines that are established by the council. In doing that, we began to see some guidelines that were not quite there," offered Mayor Daniel Evans.
Williams has been the town manager for the past two years.