If I want to mention Ministry of Health in the middle of a sentence should I capitalize initials or not. For example:
Thanks to the German Ministry of Health
Thanks to the German ministry of health
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This is a tricky one.
If the actual name of the ministry was THE GERMAN MINISTRY OF HEALTH, then you should capitalise it.
In fact it is most unlikely to contain the word German and it is equally unlikely to be in English. In all probability it is something like Gesundheitsministerium. So, in effect, you are either translating the name or describing the function of a German ministry. In such cases capitalisation would not be required. However, if I were writing a letter in English to the ministry, with its name and address at the top of the page, I would make an exception.
In this instance my inclination would be NOT to capitalise as I don't think it meets the criteria.
You might get further guidance on when to capitalise from sites such as the one below.
Primarily this question is a matter of style. Some style guides (eg The Economist) avoid capitalisation except where absolutely essential to avoid ambiguity.
Unless your chosen style guide tells you otherwise, my opinion is that you could safely refer to "the German ministry of health" in writing about, for example, the response of various national health ministries to some problem (such as coronavirus).
But if you wanted to comment on some particular feature of that ministry then you might say " the Gesundheitsministerium (German ministry of health) have always favoured vaccination [or whatever it is you want to say specifically about that organisation]".