The military said one of the outlets, Al Watan TV, is a pirate station whose frequencies interfered with legal broadcasters and aircraft communications. It said several transmitters were confiscated in the operation initiated by Israel's Communications Ministry.
The military also confirmed a second raid at Jerusalem Educational TV, a Ramallah-based station owned by the Palestinians' Al Quds University, but did not elaborate.
Palestinian officials denounced the raids as an aggression and violation of media freedoms.
The Palestinian prime minister, Salam Fayyad, visited Al Watan later yesterday and said the raid undermined his government. Mr Fayyad heads the Palestinian Authority, which runs the Palestinian self-rule areas that cover 38 per cent of West Bank territory.
"This is a clear aggression against what remains of the Palestinian Authority," Mr Fayyad said, urging international Midlle East mediators to get Israel to halt such raids.
The Al Watan station director, Moammar Orabi, said about 30 soldiers entered the station before dawn. The TV frequently reports on Palestinian protests against Israeli policies in the West Bank. It is owned by three non-governmental associations, including the Palestinian Medical Relief Society, headed by the politician, Mustafa Barghouti.
"This is an act of repression of the freedom of the media in Palestine, and of repression of the popular resistance that we believe in," Mr Barghouti said.
Also yesterday, Israeli authorities issued demolition orders against foreign-funded solar panels and wind turbines that have provided small Palestinian herding communities in the southern West Bank with electricity, according to one of the donors, the German-based group medico international.
Palestinians and Israeli rights groups allege that Israel systematically suppresses Palestinian development in that part of West Bank.