Federal workers are increasingly dismayed by what they see as weak leadership across government, according to a survey released Tuesday that finds employees’ job satisfaction at its lowest point since Congress required the first workplace appraisal 11 years ago.

Despite continued positive feedback at some agencies and improving morale at others, just 56.9 percent of employees are happy with their jobs and would recommend their agencies as places to work, the annual “Best Places to Work in the Federal Government” rankings say.

A steady drop in employee satisfaction is underscored this year by a three-point decline, to 42.4 percent, in confidence in the workplace stratum from Cabinet secretaries to mid-level managers. This poses challenges for President Obama as he pursues an immigration overhaul, tax reform, rules to limit greenhouse gas emissions linked to climate change, and other policies in his last two years in office.

For example, the Department of Homeland Security, the agency tasked with providing administrative relief and work permits to as many as 3.7 million undocumented parents and 300,000 children, ranked at the bottom of large agencies for a third year running, with employee satisfaction and commitment at 44 percent.

“If you or I are running into stresses at work, we look to our bosses to look out for our interests,” said Jeffrey Neal, who retired as DHS’s chief human capital officer in 2012 and writes a blog on federal personnel issues.

“When you see a government where people have been beaten on for years and don’t feel faith in their leaders, they start feeling, ‘I’m on my own,’ ” he said. “The effect is that people who have morale problems are not as productive.”

Lingering effects of the budget cuts known as sequestration, last year’s government shutdown, pay freezes, hiring slowdowns and a dim view of federal work among some Republicans in Congress have all contributed to the decline in morale, agency leaders said.

But experts outside government also say the administration failed to make managing the federal bureaucracy of 2 million people a priority. They also fault Congress for elevating missteps, such as the Internal Revenue Service’s targeting of nonprofit groups, to partisan issues.

“It’s a failure of attention and focus by the president and Congress on the most basic ingredient for the success of the government,” said Max Stier, president of the nonpartisan Partnership for Public Service, which puts out the annual “Best Places” rankings with the consulting group De­loitte.

J. David Cox Sr., president of the American Federation of Government Employees (AFGE), said in a statement Tuesday, “How can federal employees have anything but a low opinion of those who implement these policies?”

On Tuesday, Obama is to meet for the first time in his presidency with the Senior Executive Service, the government’s corps of 6,000 top leaders — a gathering viewed by many as long overdue.

Employees at NASA, which ranks as the best large place to work in the government, said they value their mission to continue cutting-edge research, technology and space exploration despite the retirement of the high-profile shuttle program.

“Everyone here has a lot of pride and knowledge, and they’re high-caliber individuals,” NASA flight director Mike Sarafin said. “Just being surrounded by people like that drives you to be your best.”

Sarafin was the lead flight director for last week’s Orion space flight, which is a building block for an eventual mission to Mars.

“I’m a bit of an adrenaline junkie, and working for mission control is something that gets me out of bed every day,” he said. “Last week is a good example of that.”

The Commerce Department came in second among large agencies, followed by the State Department and the intelligence community, which does not break down its responses by agency. The tiny Office of the General Counsel at the Federal Energy Regulatory Commission logged the highest score in government, with 88.8 percent of its 100 or so lawyers reporting on-the-job satisfaction.

The most dispirited employees work at the Defense Nuclear Facilities Safety Board, with just 33.8 giving positive responses, down from 45.5 percent in last year.

Overall scores improved for 43.1 percent of those surveyed. The survey’s conclusions are based on data collected by the Office of Personnel Management, which surveyed the workforce from April through June. More than 400,000 employees at 389 agencies and smaller offices responded.

Employee satisfaction with pay, which had dropped from 63 percent four years ago to 50.3 percent in 2013, edged up by 2.2 points this year, reflecting Congress’s decision to give the workforce a 1 percent raise after a three-year pay freeze. Employees also said that the government is becoming more diverse.

Yet 7 in 10 workers said their chance at a promotion is based not on merit but on favoritism. Many do not feel their work is recognized. They’re frustrated that spending scandals and flat or declining budgets have sent important training out the window.

“People feel awards are given for projects that are popular, not necessarily for the quality of the work,” said Jeff Bratko, a scientist at the Environmental Protection Agency’s air-enforcement division in Chicago and a local AFGE representative. “If someone’s really toiling away doing the day-to-day work of the agency, it seems like those things don’t get recognized.”

The rankings have come to serve as a road map for Cabinet secretaries, particularly as hiring has slowed in recent years. Improving employee “engagement” is a priority in the president’s management agenda.

At the Department of Housing and Urban Development, which ranks last among midsize agencies, Bill Amos said he sees a generational divide in the workforce.

“There’s an old guard of workers who’ve been here a long time who feel nothing will ever get better, and they aren’t budging,” said Amos, who leads a small broadcast team.

He said that “there’s a huge push at the senior level to address why people are unhappy.” The agency recently offered employees memberships in the Capital Bikeshare program. “That fell under the message of trying to make sure everybody knows the survey matters,” Amos said.

When Thomas Perez took over as secretary of labor in July 2013, he and his leadership team set out to raise morale at an agency that had ranked near the bottom of the “Best Places” list for several years. They started one-on-one meetings with employees, a suggestion box for new ways to do business and a program that offers employees a chance to work for several months in a different office or job within the agency.

“This is an agency that has been under attack from Capitol Hill on many issues, including funding,” Deputy Secretary Chris Lu said in an interview. “But the secretary has made a point of telling employees, ‘The work you do is critical.’ ”

The DHS saw its scores drop by nearly three points from last year, with the steepest decline in the area of senior leadership. Over the past four years, the department has lost employees at nearly twice the rate of the federal government overall.

Soon after taking office, Homeland Security Secretary Jeh Johnson and Deputy Secretary Alejandro Mayorkas created an employee steering committee focused on fairness in hiring and promotions and restarted a program that honors outstanding workers. Johnson handed out distinguished-service awards to more than 300 workers at a ceremony in October.

At the Commerce Department, Secretary Penny Pritzker said managers are “given permission to give bad news” rather than reprimanded for bringing problems to the surface.

For example, after The Washington Post reported in the summer about fraudulent time and attendance practices at the Patent and Trademark Office, Pritzker said she “empowered [Deputy Undersecretary] Michelle Lee to understand the challenges.”

“The approach was, ‘How are we going to fix this, and what are the resources we think we ought to bring to bear?’ ” Pritzker said. “Stuff’s going to go wrong. We have to acknowledge that.”