Jalil Khan says 48 people died Friday in the dispute over access to water in the Kurram region.
There have been frequent bouts of deadly tribal and sectarian fighting in the region over the last few years.
Khan says one tribe consists of minority Shia Muslims while the other is Sunni.
Kurram and other parts of the border region are also home to Sunni Islamist militants and al-Qaida.
Some reports from the remote region have said the militants may have a role in the conflict.