Clouds are reflected in the Capitol reflecting pool at daybreak in Washington. (J. David Ake/AP)

Federal employees who were put on unpaid furloughs during the partial government shutdown will be paid for that time, under the legislation signed late Monday ending the shutdown.

It says employees sent home without pay “shall be compensated at their standard rate of compensation, for the period of such lapse in appropriations, as soon as practicable.” That follows the practice of past shutdowns in which all employees were paid as normal, regardless of whether they continued working or were furloughed.

Although relatively short-lived by the standards of its predecessors in 1995-1996 and 2013, the three-day shutdown that started Saturday had a similarly complex effect on the federal workforce.

In some cases, employees continued working with a guarantee of no interruption in pay, because the agency — or their part of it — does not depend on annual appropriations for funding.

Those in agencies funded by annual appropriations but who were kept at work because of the nature of their job were guaranteed to be paid, though not until funding was restored. Those furloughed also are guaranteed to be paid eventually for the time they spent shutting down their work. The “continuing resolution” language covers the time they were furloughed, in most cases about half of Monday.

Though all employees are now guaranteed to be paid in full, it may not happen on their regular schedule. Most federal employees work on a two-week pay cycle that ended Saturday, although others are under different pay cycles. Pay is not actually distributed until a number of days after a pay cycle closes.

After the 2013 shutdown, the Office of Personnel Management issued extensive guidance to sort out the complexities. No similar guidance had been issued as of midday Tuesday.

One of the largest federal payroll processors, the Defense Finance and Accounting Service, said Tuesday that it will post information about the impact “as soon as possible.” In addition to paying military personnel and Defense Department civilian employees, that agency handles payroll for several departments, including Energy, Veterans Affairs and Health and Human Services, among other agencies.

Granting back pay to those furloughed means that “federal employees will not have to suffer financially for the three-day shutdown. All federal employees, whether they were furloughed or excepted, are counting on a full paycheck, on time, in order to pay their bills,” said Tony Reardon, president of the National Treasury Employees Union.

Richard G. Thissen, president of the National Active and Retired Federal Employees Association, said his organization “applauds the funding deal’s inclusion of back pay for those federal workers who were unable to go work during the shutdown. We cannot allow our nation’s civil servants to be collateral damage in congressional gridlock and we thank those who voted to provide back pay.”

“Americans deserve to be able to access the programs and services that their tax dollars have funded, and federal employees deserve to be able to go to work without wondering when or if they will get paid,” said American Federation of Government Employees President J. David Cox Sr. “I do want to thank lawmakers for ensuring that federal employees who were impacted by the shutdown do not lose any pay. Federal employees and their families should not be forced to go without pay when they are not allowed to do their jobs because Congress cannot pass a funding measure.”