At least 21 people were killed and 70 hurt in the suspected suicide attack, which happened during a New Year's Eve service at the al-Qiddissin Church.
In a rare televised address, Mr Mubarak said it bore the hallmark of "foreign hands" seeking to destabilise Egypt.
Several hundred Christians later clashed nearby with Muslims and police.
There was no claim for the attack but Al-Qaeda has called for punishment of Egypt's Copts over claims that two priests' wives they say had converted to Islam were being held by the Church against their will.