The Israeli military said the attacks were pinpoint strikes on Hamas communication devices located on the buildings' roofs, and accused the Islamist group of using reporters as human shields to try and protect their operations.
Britain's Sky News, German ARD, Saudi-owned Al Arabiya, Beirut-based al Quds television and other broadcasters operate from the two buildings, which are a block apart. One employee from al Quds TV lost his leg in the early morning strike.
The attack came on the fifth day of heavy air strikes on the coastal enclave which Israel says are needed to halt repeated militant rocket launches into its territory.
The Foreign Press Association covering Israel and the Palestinian Territories issued a statement in which it expressed concern over the bombings and quoted a U.N. Security Council resolution that condemned attacks against journalists.
Israeli military spokeswoman Avital Leibovich denied that journalists were the target of the strike.
"Hamas took a civilian building and used it for its own needs. So the journalists ... were serving as human shields for Hamas," she said.
The military added that in order to avoid worse casualties, it had refrained from firing at an Hamas operations room which it said was located inside one of the buildings.
Abdel-Ghani Jaber, director of a private Palestinian media production company, said two of his employees were wounded when the blast shattered the windows of his office.
"I was asleep when it happened ... I jumped from the mattress because it sounded so near," Jaber said, "I wanted to look out the window when someone told me the building was being bombed and I started to run. As I ran a second missile hit just above our floor and damaged a room in my office."
In the West Bank city of Ramallah, journalists held a protest against Sunday's strikes. Palestinian government spokeswoman Nour Odeh said the attacks were "a clear message against the freedom of journalism and opinions".
The Palestinian Centre for Human Rights condemned the raid and said that: "Israeli forces jammed the broadcasts of a number of local radio stations."
An Israeli military spokesman said the army had cut into a Hamas radio frequency on Sunday and used it to broadcast warnings to residents to get away from Hamas properties and avoid becoming casualties.
In a 2008-2009 war against Hamas, Israel attacked one of the same buildings that was blasted on Sunday, again accusing Islamist militant of operating out of the tower block.