As with all prayers, it is a requirement for the funeral prayer that anything impure which would prevent the validity of the prayer (removal of impurities) be cleaned. Accordingly, if there is nothing impure on the shoes of the person performing the funeral prayer, there is no religious objection to praying with shoes on. Indeed, the Messenger of Allah (peace be upon him) stood for the funeral prayer with his shoes on, and only removed them when Gabriel informed him that there was impurity on them (Abu Dawud, Salat, 89 [650]).
Source: T.C. Diyanet İşleri Başkanlığı, Din İşleri Yüksek Kurulu
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