It's true - they will say, "Too bad, it's your problem" and they'll delay processing of the application. I really hate it when ex-spouses refuse to try to understand this part of the process, and that complying is in the best interest of the child.
I would try to send this information from the
CIC Family Class Processing Manual, Sections 5.10-5.11 to your ex - maybe it will help explain to him why you're asking for this, and also reassure him that this doesn't mean you're going to try to sneak back to Germany and kidnap your son to Canada. You would never be allowed to bring him into the country, even for a visit and even if/after he is examined, without his father's written authorization.
5.10. Non-accompanying family members
Applicants must declare all family members when applying for a visa and must again declare all family members, whether accompanying or not, prior to obtaining permanent resident status. Permanent residents who did not declare all their family members on their application are reportable under A44(1) [see also “Sponsor who may be subject to an A44(1) report” (section 10.5 below) and “Misrepresentation” (section 5.22 below)].
In addition, all family members, whether accompanying or not, must be examined, unless the appropriate officer determines that they are not required by the Act or the former Act to examine the family member [R117(10)]. Family members who were not declared and examined are excluded from the family class and may not be sponsored at a later date as per R117(9)(d) unless R117(10) applies.
Non-accompanying family members must undergo medical examinations. They must also establish that they are not inadmissible for criminal or security reasons. If the requirement for minimum necessary income is applicable, sponsors must demonstrate that they can support all family members, including non-accompanying family members. Non-accompanying family members need not be in possession of a passport or travel document.
5.11. Inadmissibility and non-accompanying family members
All family members, whether accompanying the principal applicant or not, are required to be examined unless an officer decides otherwise. Normally, an inadmissible family member, whether accompanying or not, would render the principal applicant inadmissible. There are, however, two exceptions to this rule described in R23. The first is the separated spouse of the applicant and the second is where a child of the applicant who is in the legal custody of someone other than the applicant or an accompanying family member of the applicant, or where someone other than the applicant or accompanying family member of the applicant is empowered to act on behalf of that child by virtue of a court order or written agreement or by operation of law. If an applicant's separated spouse or their children who are in the custody of someone else are inadmissible, their inadmissibility would not render the applicant inadmissible. Because separated spouses can reconcile and custody arrangements for children may change, examination is required in order to safeguard the future right to sponsor them in the family class. If these family members are not examined, they cannot be sponsored in the family class in the future under R117(9)(d) unless R117(10) applies. Satisfactory documentary proof of a separation and of custody being with someone other than the applicant is required. A separation agreement or custody papers are examples of acceptable proof.
Officers will not issue a permanent resident visa to separated spouses, common-law partners or children in the custody of someone else, even if they are examined. This is because separated spouses and partners are not members of the family class as per R117(9)(c) and because children in the custody of someone else are non-accompanying family members."
As you can see, CIC is very clear that they will not issue visas to children who are in the custody of the other parent, but it's true that if your son is not examined, he becomes ineligible to be sponsored at a later date if something should happen to his father. That's a tough position for his Dad to put your son in. Unfortunately, you're going to have to get tough about this and maybe even go to Court to compel his father to allow the medical examination if he can't be convinced. CIC does not like to let parents leave minor children in another country with an ex-spouse without doing their best to compel examination. And CIC will get in touch with your ex and try to get him to consent. Maybe if you show him you have no other choice and you offer to pay for the examination, he'll relent. Good Luck.