Under german employment law, three days does not constitute this type of action. However, if there is proof of continued three-day illnesses and the certificate signed by the same physician can cause suspicion. it can therefore be justifiable if documented.
So, this might be a new standard that your employers are trying to implement, and with enough justification, we all know that they can and will get this integrated into their standard operations procedures for employment agreements.
If you have nothing to worry about, I would go and let them examine you - but they should pay for the examination since it is the employer's wish.
Who know, you might be written sick longer than the three days, and at their expense.
Good luck, and keep us posted.

Unfortunately, in the Human Resource business, things are going to change and we will have to get used to it.