In European patent practice, a claim in the form "Substance X for use as a medicament" is acceptable, even if X is a known substance, but its use in medicine is not known.
Likewise, it is acceptable to have a claim in the form "Substance X for use in the treatment of disease Y", provided that such a claim involves an inventive step over any prior art disclosing the use of X as a medicament.

In Japan, a patent examiner interprets "Substance X for use in the treatment of disease Y" in Claims as "Substance X" itself without limitation of use because the expression "for use in the treatment of disease Y" only indicates the utility of the substances in consideration of the statements of the description and drawings as well as the common general knowledge at the time of filing.

Thus, an applicant should modify claims in order to conform Japan patent practice if claims contain such medical use claims.  Specifically, the substance should be changed to a composition (or a pharmaceutical composition) comprising the substance.
Examples of claims are shown below.

Claims

1. Substance X for use in the treatment of a malignant tumor.
(悪性腫瘍の治療における使用のための、物質X。)
2. A pharmaceutical composition for use in the treatment of a malignant tumor, comprising a compound X.
(化合物Xを含む、悪性腫瘍の治療における使用のための医薬組成物。)
3. A pharmaceutical composition for treating a malignant tumor, comprising a compound X.
(化合物Xを含む、悪性腫瘍の治療用医薬組成物。)
ClaimsAnalysis 
1BadAn examiner interprets that Claim 1 is directed to a substance itself without limitation of medical use. Thus, the limitation of medical use does not contribute to patentability (novelty and inventive step).
2GoodAn examiner interprets that Claim 2 is directed to a composition with limitation of medical use. Thus, the limitation of medical use contributes to patentability (novelty and inventive step).
3GoodAn examiner interprets that Claim 3 is directed to a composition with limitation of medical use. Thus, the limitation of medical use contributes to patentability (novelty and inventive step).
Additional information on medical use claims is described on another page (Link).
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