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The pair join Jamie Smith, Barry Nicholson, Michael Hart, Richie Byrne and Ryan Esson on the sidelines.
Diamond has already withdrawn from the Scotland Future squad who host Turkey in Inverness on Wednesday with an ankle injury, while Scotland international McNaughton picked up a thigh problem during Saturday's losing game against Dunfermline.
Dons boss Jimmy Calderwood is preparing for the weekend's game on the basis that he will be without the pair.
He said: "Both of them could be out for next weekend, we don't know at the moment. It could mean having to shuffle things about again to compensate for losing two of our key defenders."
Please Jimmy: no more ^*&%ing shuffling! We beg you.