Sometimes the only thing worse than having an HR department is not having one.

When LRN Corp., which helps companies develop ethics and compliance programs, restructured a few years ago, the 250-employee business abolished most job titles and department names. It also did away with its human-resources department, which had dealt with recruiting and compensation issues, among other things.

"We wanted to force the people issues into the middle of the business," said David Greenberg, Los Angeles-based LRN's executive vice president.

Companies seeking flat management structures and more accountability for employees are frequently taking aim at human resources. Executives say the traditional HR department—which claims dominion over everything from hiring and firing to maintaining workplace diversity—stifles innovation and bogs down businesses with inefficient policies and processes. At the same time, a booming HR software industry has made it easier than ever to automate or outsource personnel-related functions such as payroll and benefits administration.

Some workers say they feel the absence of an in-house HR staff acutely, especially when it comes to bread-and-butter HR responsibilities such as mediating employee disputes and resolving pay problems. LRN and other companies that are going it alone say they are working out the glitches as they go.

Ruppert Landscape Inc., an 11-year-old landscaping company with 900 employees, has never had a traditional HR department. Instead, managers must balance renewing contracts and ensuring that a client's grass is cut to the proper height with hunting down talent at college recruiting sessions and teaching employees about the company's 401(k) plan.

CEO Craig Ruppert said the decentralized structure fosters autonomy and accountability among leaders across the company, which is based in Laytonsville, Md., and covers markets from Philadelphia to Atlanta. He estimates that its managers spend 5% of their time on matters related to human resources.

"I just have a hard time understanding how somebody in an office two or four states away can do a better job of solving an employee problem than someone who has a vested interest in the employee," Mr. Ruppert said.

In 2012, U.S. employers had a median of 1.54 HR professionals for every 100 employees, up slightly from a low of 1.24 in the recession year of 2009, according to the Society for Human Resource Management. They earn a median annualized wage of about $51,000, government statistics show.

Startups usually launch without personnel teams, but SHRM advises that companies bring on a human-resources staffer once they reach 15 employees, the point at which personnel issues become complex enough to require specialized skills.

"Whenever you consider eliminating portions of HR you have to think of the financial risk, the strategic risk," said Steve Miranda, the managing director of Cornell University's Center for Advanced Human Resource Studies and a former HR executive at Lucent Technologies, now part of Alcatel-Lucent.

Managers often lack specialized knowledge that is crucial for keeping a company competitive and on the right side of the law, he said. If they don't understand the latest rules under the Family and Medical Leave Act, for example, they can open their company up to lawsuits; if they don't know where to find qualified engineers, they can end up behind in the battle for talent.

Outback Steakhouse, a unit of Bloomin' Brands Inc., had no HR department before 2008 but created one not long after the Equal Employment Opportunity Commission sued the restaurant chain for sex discrimination. In 2009, Outback paid $19 million to settle the case and agreed to add an executive-level HR position.

Interpersonal issues must be handled differently when HR isn't around to mediate. Klick Health, a Toronto-based marketing agency focused on health care, has forgone a human-resources department partly in favor of two "concierges," employees with customer-service backgrounds whose job is to create what CEO Leerom Segal calls a "frictionless" work experience for employees.

For the concierges, that means chores ranging from setting up mentoring sessions and career-development paths to picking up a birthday gift for a worker's spouse.

When co-workers can't stand each other or employees aren't clicking with their managers, Mr. Segal expects them to work it out themselves. "We ask senior leaders to recognize any potential chemistry issues" early on, he said, and move people to different teams if those issues can't be resolved quickly.

Former Klick employees applaud the creative thinking that drives its culture, but say they sometimes felt like they were on their own there. Neville Thomas, a program director at Klick until 2013, occasionally had to discipline or terminate his direct reports. Without an HR team, he said, he worried about liability.

"There's no HR department to coach you," he said. "When you have an HR person, you have a point of contact that's confidential."

"We aim to create a culture of openness so that all our employees can feel comfortable turning to their manager or our management team for questions, assistance, and coaching on conflict resolution or any other area," said Klick's Mr. Segal.

And though managers sometimes perceive personnel departments as slowing a company down, doing without them can lead to stagnation, according to a former LRN employee.

The company's hiring process, for example, became a lengthy and convoluted ordeal, she said, as employees labored to figure out what skills and salary a new worker should have. And the company's executives became "the ultimate decision makers for everything," she said, creating a bottleneck.

Mr. Greenberg from LRN said the company "is definitely a work in progress," and that its own metrics show it must do more to foster trust among workers. He added that the company has just brought on an employee "to focus on all things related to people at LRN."

She isn't called a human-resources executive, though; she has no title at all.

Corrections & Amplifications 

In an earlier version of this article, David Greenberg, executive vice president of LRN Corp., was referred to incorrectly in one reference as the CEO. Separately, Klick Health employs two concierges who are part of what the marketing agency calls its five-person "mojo team." A previous version of this article didn't refer to the five-person team.