President Porfirio Lobo Sosa said the military would remain at the prison until further notice, Diario Tiempo reported.
"The armed forces [will] have an immediate presence in the national penitentiary to give support to the authorities in charge of the center," Communications Minister Miguel Angel Bonilla said
Hondo Diario reported three prison guards were among at least a half-dozen people seriously injured in the clash between inmates, including gang members. Some prisoners were armed with AK-47 assault rifles and at least one grenade detonated, El Heraldo reported.
The Friday afternoon riot came a day after the release of a special report by the Inter-American Commission on Human Rights in Washington that found inmates effectively hold control of Honduras' overcrowded and corrupt prisons.
The BBC reported government figures show there are more than 12,000 inmates in prisons meant to accommodate about 8,000. There are about 3,300 prisons in the national penitentiary, located north of Tegucigalpa.