"The Ethiopian army combed the countryside, summarily executing men in front of their families while beating, raping or killing the women," the ONFL statement said.
"The ruthless troops have so far massacred 71 innocent civilians with impunity while wounding and torturing hundreds."
The Ethiopian government denied the accusations.
"We are still gathering information about these accusations, but so far we can say they are entirely baseless," Shimeles Kemal, an Ethiopian government spokesman, said.
He denied that military operations were taking place in the Ogaden area.
Claims from either side are almost impossible to verify, as journalists and aid groups cannot travel in the poverty-stricken region without a government escort.
The ONLF has been fighting for what it calls autonomy for ethnic Somalis in the Ogaden region since 1984.
The conflict has taken on new significance since international petroleum companies began searching for oil and gas in the area.
In April, a British geologist working for a subcontractor of Petronas, a Malaysian oil giant, was shot dead there.