Nuevo Leon state Governor Jaime Rodriguez said 12 other people were injured in Topo Chico jail after prisoners fought with "sharp weapons, bats and sticks".
A fire was also started in a storage room. Officials say the situation is under control and no inmates escaped.
Crowds of relatives outside the jail blocked roads, demanding information.
Some threw sticks and rocks and tried to pull the prison gate open as riot police blocked their way.
"They haven't told us anything," said the mother of one inmate, who gave her name only as Ernestina.
"They said that until there is order they won't let us in. Everything is in disorder, and nobody is telling us anything."
The incident comes just days before Pope Francis is due to visit a prison in the northern city of Ciudad Juarez, an area notorious for violence between drugs cartels.
Mr Rodriguez had earlier put the number of inmates killed at 52 before revising the figure down.
The reason was not made clear, but several inmates are registered more than once at the prison, with different names.
Forty of the 49 prisoners have already been identified.
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