During the partial government shutdown, employees generally fell into three categories: “exempt” because their agency had operating money through self-funding, trust funds or other sources; “excepted” because even though funding for their position had lapsed they were kept at work for security, law enforcement, health or other reasons; and “non-excepted,” who were put on unpaid furloughs.

No accounting has been made of the various categories although in general agencies followed the same policies that were used in 2013, when about 800,000 employees were furloughed out of the 2.1 million executive branch employees apart from the self-funding USPS and intelligence agencies.

Rules on Government Furloughs [ ask.FEDweek.com ]

The measure ending the shutdown provided that all federal employees be paid as normal, as had been done in prior shutdowns. That primarily benefits “non-excepted” employees, who were guaranteed to be paid only for the time they had worked to shut down, in most cases for part of the day Monday. “Excepted” employees were guaranteed to be paid in any event for the time they worked, although they were working without pay for the meantime, until funding was restored. The shutdown had no impact on pay for employees in exempt agencies or operations.

However, the timing of the shutdown caused complications. Most employees work under a pay cycle whose last day, Saturday January 20, was the first day of the shutdown–and thus the shutdown spanned a small part of two pay periods. The payroll distribution for a biweekly period in most cases is made about a week after the period ends, but there are variations. In addition, some employees are under different pay cycles with yet different pay distribution dates.