I would tell the city manager the truth, but maybe not the whole truth.

What I mean is I would leave out the details. Perhaps only mention something about extenuating circumstances that prevent him from covering his shifts. I would leave it kind of vague, but peaking his interests. And when/if he tries to question you about it. I would state that you do not feel it is your place to discuss issues in your boss's personal life, but it would be in his (the city manager's) best interest to have this conversation with your boss. Something like, "It is not a health issue. But I feel that is not my place to discuss his personal issues and I think it is best that you have the conversation about the details with him." I expect that someone in his position would have some experience with H.R. issues and will respect your position, be pleased that you alerted him to "a situation" (that is really his responsibility to look into), and know how to handle it.

After all, depending the policies of your company/employment, I believe you are probably not under any obligation to disclose this information about a co-workers personal life. Just be honest about your boss's request, be vague about the details (since you really don't know all the circumstances, anyway), and suggest that the city manager discuss this issue with your boss.

And, depending on the job functions of your boss, I would simply state that you are happy to fill in for him as he requested and feel you are up to the task (blah, blah, blah), but that you feel that your then supervisor (city manager, or whoever) should be aware of the situation (professionally, as it relates to your work only) and that you want to ensure that you have the support of your supervisor for any decisions you have to make for your detained boss, since you will be filling in for your boss after such a short time with the company.

This is kind of the way I would handle it. But I'm not in you shoes and you'll have to "read" your situation for yourself

GL