It is not permissible for graves to be left in mosques, whether that is the grave of a wali (“saint”) or of anyone else, because the Messenger (PBUH) forbade that and warned against that, and he cursed the Jews and Christians for doing that. It was narrated that he (PBUH) said: “May Allah curse the Jews and the Christians, for they took the graves of their Prophets as places of worship.” [Bukhaari, 1330, Muslim, 529]
He (PBUH) also said: “When a righteous man died among them, they would build a place of worship over his grave and put those images in it. They are the most evil of mankind before Allaah.” (Al-Bukhaari, 427; Muslim, 528)
He(PBUH) said: “Those who came before you took the graves of their Prophets and righteous people as places of worship. Do not take graves as places of worship – I forbid you to do that.” (Narrated by Muslim in his Saheeh, 532, from Jundab ibn ‘Abd-Allaah al-Bajali).
So the Prophet (PBUH) forbade taking graves as places of worship and he cursed those who do that, stating that they are the most evil of mankind. So we must beware of that.
It is known that everyone who prays at a grave (Dargah) is taking it as a place of worship, and whoever builds a mosque over a grave (Dargah) has taken it as a place of worship. So we must keep graves far away from the mosques and not put graves inside mosques, in obedience to the command of the Prophet (PBUH) and so as to avoid the curse issued by our Lord against those who build places of worship over graves, because when a person prays in a mosque in which there is a grave, the Shaytaan tempt them to call upon the deceased or to seek his help, or to pray to him or prostrate to him, thus committing major shirk (polytheism) and going out of fold of Islam.
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May ALLAH forgive our sins... Ameen