First, check with the Reporting Manager on why this employee preferred to send the resignation letter during their absence from work. Could this be the result of any awkward situations between both of them? Or was this a one-off situation with just this employee?
While for any Reporting Manager, this may be just about normal, as HR, you need to focus on the long-term aspects of such situations. What if this becomes a precedent?
Also, put timelines for the Manager's response to the issue. But as HR, it's your job to communicate with the employee in such matters.
When you respond to the resignation, do it through email too, and then follow up with a call. Cover the various aspects of the notice period, etc., that every employee needs to adhere to. Insist that there needs to be a meeting ASAP to decide the next step—like Dishkit suggested/mentioned.
All the best.
Regards, TS