The first aspect which we must determine is under which head of income, the particular property is chargeable. The provision for depreciation can be ONLY allowed if the income generated from the asset is classified under "profits and gains from business or profession."
If the companies object is in line with the business of renting properties or like, then the income can be safely parked under this head. Then depreciation must be charged in the profit and loss account and like wise in ITR too.
On the contrary, if the objects of the company has no nexus with the property income. Then the income must be classified under "Income from house property". In this case, depreciation may be charged under the companies act 2013. However, no depreciation can be charged under the Income tax act and ITR you will not be able to claim depreciation. Showing the asset in balance sheet is only incidental to the taxing provisions.
Hope I have clarified your query.