The Ruling on Praying in Mosques which contain Graves

Question:

Is prayer in mosques which contain graves accepted?

Answer:

Mosques containing graves are not to be prayed in. It is obligatory that those graves be exhumed and the remains be reburied in the public graveyards, each grave in a separate hole, like the rest of the graves. It is not correct to allow graves to remain in them, whether it be the grave of a Waliy, or any other grave, because the Messenger forbade, warned and rebuked the Jews and Christians from doing so. It is authentically reported from him that he said:
"Allah cursed the Jews and Christians (because) they took the graves of their Prophets as places of prayer.

'A'ishah, may Allah be pleased with her, said: "He warned against what they did." (Narrated by Al-Bukhari and Muslim) And he said, when Umm Salamah and Umm Habibah, may Allah be pleased with them both, informed him about a church in which there were pictures and such like,
«Those people, when a righteous man among them died, would build a place of prayer over his grave and they would decorate it with those pictures. They will be the worst of people before Allah on the Day of Resurrection.

And he said:
«Verily, those who were before them used to take the graves of their righteous folk as places of prayer. So do not take the graves as places of worship, for I forbid you to do so.

So he forbade them from taking the graves as mosques. It is well known that when a person prays by a grave, he has taken it as a mosque, and whoever erected a building over a grave in order to pray therein has taken it as a mosque. It is obligatory that graves be away from mosques and that graves not be placed in them, in obedience to the orders of the Messenger and in order to avoid the curse of our Lord, the Almighty and Majestic, which is upon those who build over graves. For should one pray in a mosque containing graves, Satan may entice him to supplicate to the dead, or seek help from them, or pray to them, or prostrate to them. In which case, he will have committed major Shirk, for this is one of the deeds of the Jews and Christians, so it is an obligation upon us to differ from them and stay away from their ways and evil deeds. And Allah is the Granter of success.

Source:
Fatawa Islamiyah, Vol. 1 Pages 148-149