Twenty years after the Family and Medical Leave Act became a national law, many employers still struggle to correctly apply several of its rules.

Enacted on Feb. 5, 1993, the FMLA allows eligible employees up to 12 weeks of unpaid leave a year in cases of serious illness or injury, or to care for sick or injured family members.

Generally, employers have not found FMLA compliance to be overly burdensome, according to a study the U.S. Department of Labor released last week marking the 20th anniversary of the law.

However, issues such as requests for intermittent leave, employee notice requirements and certification procedures, as well as the statute's interaction with other laws, continue to present considerable challenges for many employers, experts say.

“Without question, the No. 1 issue that employers struggle with is managing unscheduled, intermittent leave,” said Jeff Nowak, a Chicago-based partner at law firm Franczek Radelet P.C.

According to the labor department's survey, 41% of employers offering FMLA leave said administering intermittent leave was somewhat or very difficult. Primarily, Mr. Nowak said employers find it challenging to determine when intermittent leave is appropriate, as well as obtain accurate, adequate information to confirm the validity of an employee's reason for requesting the leave.

“Because intermittent leave can be taken in small increments, it lends itself to abuse, and that can cripple an employer's operations,” Mr. Nowak said.

Employers also struggle with the law's rules governing notification and certification requirements for employees, though the percentage of companies reporting difficulty with those provisions has shrunk considerably since 2000, according to the Labor Department study.

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In 2008, the Labor Department issued revised regulations clarifying employers' rights to require formal notification of leave requests from employees, as well as medical certification of their reasons for requesting leave. The revised rules permitted employers to require eligible employees to submit written notice of their FMLA leave requests to a designated leave administrator.

“Previously, it was sort of up for grabs,” said Ellen McLaughlin, a Chicago-based partner at Seyfarth Shaw L.L.P. “Employees could simply tell their manager they were taking leave, and that was good enough. But the managers weren't trained, so they wouldn't know what kinds of leave are permissible under the law.”

The 2008 regulations also clarified employers' rights to obtain medical certification for FMLA-qualified leave requests, as well as the types of information they can demand from employees and their health care providers.

Despite the clarifications, nearly 20% of employers surveyed by the Labor Department in 2012 said navigating the law's notification and certification provisions was somewhat or very difficult.

Ms. McLaughlin said several of the revised rules have been challenged in civil courts. It remains to be seen how those cases will inform notice and certification requirements going forward.

Another persistent concern for employers is the extent to which the FMLA interacts — and in some cases, conflicts with — other federal, state and local laws. In the early years following the FMLA's enactment, it was widely accepted that qualified leaves of absence would satisfy an employer's obligations under the Americans with Disabilities Act, as well as corresponding state and local statutes.

“That clearly is no longer the case, and what employers are left with is a three- or four-pronged obligation to assess what constitutes a qualifying medical claim or disability,” said Ricki Roer, a New York-based partner at Wilson Elser Moskowitz Edelman & Dicker L.L.P.