A crowd of relatives of the inmates at the Port Said penitentiary stormed the facility with rocks and Molotov cocktails and had to be beaten back by police with tear gas.
The military source said five Egyptian soldiers had to be treated for the effects of the gas, but the authorities remained in control of the scene.
The Port Said prison has been the scene of repeated violent protests over the death sentences handed out to 21 defendants in a major soccer riot in Port Said last winter that left 72 other fans dead.
Another round of sentences will be handed down March 9. Ahram Online said the government planned to transfer all of the Port Said inmates to different and unidentified facilities before then, which apparently contributed to Sunday's clashes.