Police began guarding walls of sandbags along the Lagan River after about 500 went missing, the newspaper said. A source said members of the Ulster Volunteer Force were involved in the theft.
There were reports bags were being offered for sale for 1.5 pounds (about $2.50) each in East Belfast, where flooding was forecast.
"If people have been taking property like that and trying to make a profit I think it is morally reprehensible," Assistant Chief Constable Stephen Martin of the Police Service of Northern Ireland said. "I think they are damaging their own community, and if anyone has evidence of that we will certainly look to establish whether a criminal act has taken place."
The UVF, founded at the beginning of the Troubles in the mid 1960s, has remained active since the 1994 cease-fire, although much of its energy has been spent feuding with other loyalist militias. UVF leaders are believed to have been involved in rioting in December 2012 over flying the British flag at Belfast City Hall.