Your organization can (and should) establish clear rules for whom employees should contact if they need time off. Those rules can specify one contact person for run-of-the-mill absences and a separate contact for-related time off. That way, HR can collect the information it needs to assess FMLA eligibility, but it isn't overwhelmed with daily notice of late arrivals and minor illnesses.
For example, you can require employees who are late or out sick with a minor illness to notify a supervisor or receptionist, but require those who needto notify the HR office. Include written policies in the employee handbook and remind employees of that duty regularly with paycheck envelope inserts.
Recent case: After construction worker Terry Walton twisted his knee, he called his employer's security office to report that he would need a day off to see the doctor. The doctor told Walton he had a torn ligament and would need a month off, so Walton called the security office again to report that he'd be out a month.
Company policy allowed employees to call the security office if they'd be missing a day for minor illnesses or other emergencies. But the policy said employees should contact HR if they needed to be out for longer periods and might need FMLA leave. (Employees were reminded once a year via pay-envelope memos that they shouldn't request FMLA leave through the security office.)
Walton was fired since he didn't show up for weeks and hadn't told HR or any supervisors that he needed FMLA leave. He filed an FMLA suit, but the court sided with the company, saying its policy met a legitimate business need to track leave requests. (Walton v. Visteon Corporation, No. 04-1471, 6th Cir., 2005)