The furloughs were expected to be spread across the board but federal employees have learned that administering the furloughs is uneven, The Washington Post reported.
The furloughs are expected to begin in about three weeks and affect about half of the federal workforce of 2 million people, officials said.
Some agencies benefited from exceptions Congress put in legislation to keep the government going through Sept. 30, the end of the current fiscal year. Other agencies, such as the Pentagon, were given the authority to shift money around.
Some employees must wait while other agencies hone plans or finish bargaining sessions with unions, the Post said.
As of late Thursday, more than 100,000 Justice Department employees were told they would have to wait until mid-April to learn whether they will be furloughed after having been told in February to expect 14 unpaid days.
Examples of how some agencies have addressed the sequester include:
Every U.S. Park Police officer will be off the job for 14 days even though the national parks they patrol will be staffed.
The Department of Housing and Urban Development will close for seven days in May after determining staggered furloughs for 9,000 employees would create too much paperwork.
The Pentagon said it would cut its planned furlough days from 22 to 14.
Both sides have recognized that the disruption isn't federal managers' fault but that hasn't stopped the American Federal of Government Employees from filing an unfair labor practice complaint against the Environmental Protection Agency this week after management rejected the union's demand to bargain over some issues, saying it arrived too late, the Post said.
Unions did post some wins, the Post said. Most agreements guarantee an employee's performance review wouldn't be negatively affected because of project delays and telecommuting has been protected. Also, employees can choose their days off as long as their supervisor agrees, with seniority determining who can take off Mondays and Fridays.