The outlawed Kurdistan Workers' Party (PKK) militants launched rockets at a passing armoured police vehicle in the Bismil district of the Kurdish majority Diyarbakir province, the sources told AFP.
But the rockets missed their intended target and hit a three-story house, killing the girls, aged nine and 12.
The Turkish government has been waging an offensive against PKK strongholds in the southeast and in neighbouring northern Iraq.
In response the group -- blacklisted as a terrorist organisation by Turkey and much of the international community -- has launched bloody attacks on security forces.
The spike in violence between Kurdish militants and Turkish security forces since July has left a two-year ceasefire in tatters.
Over 40,000 people have been killed since the PKK took up arms in 1984 demanding an independent state for Kurds. Since then the group has narrowed its demands to greater autonomy and cultural rights.