Abu Akleh was one of Al Jazeera's first field correspondents, joining the network in 1997. She was hit by a bullet while covering Israeli raids in the city of Jenin in the occupied West Bank.
After being shot, she was taken to hospital in a critical condition and died soon afterward, the Palestinian Health Ministry and Al Jazeera journalists said.
The Israeli army attributed her death to fire from Palestinian forces in a clash with Israeli soldiers. However, Al Jazeera's Ramallah bureau chief Walid al-Omary said there had been no shooting by Palestinian gunmen.
The Palestinian Journalists Syndicate (PJS) said that this crime was "deliberate and planned to assasinate her".
"There are a few testimonies from the journalists who were with her when she was killed, saying that they were moving as a group, all wearing journalists' gear and clearly identified when they were shot at by Israeli snipers, they were the only group in the street. There were no demonstrators or exchange of fire", the union said in a statement.
Videos of the attack show that Abu Akleh was shot in the head, said Al Jazeera’s journalist Nida Ibrahim.
"What we know for now is that the Palestinian health ministry has announced her death. Shireen Abu Akleh, was covering events unfolding in Jenin, specifically an Israeli incursion into the city, which is in the north of the occupied West Bank, when she was hit by a bullet in the head," said Ibrahim, speaking from the Palestinian city of Ramallah. "As you can imagine, this is a shock for the journalists who have been working with her." She was a "highly respected journalist", she added.
Al Jazeera producer, Ali Samoudi, was also shot in the back with a live bullet. Samoudi is reported to be in stable condition.
Giles Trendle, managing director of Al Jazeera English, said the network was "shocked and saddened" by the death of Shireen Abu Akleh and called for a transparent investigation into her murder.
"As journalists, we move on. Our mission is to move forward. We will not be silenced despite attempts to silence us," Trendle said. "Our mission is to continue to inform the world of what is happening. And that is more important than ever".
The IFJ has recently submitted a case to the International Criminal Court (ICC) alleging that Israel’s systematic targeting of journalists working in Palestine and its failure to properly investigate killings of media workers amount to war crimes.
IFJ General Secretary Anthony Bellanger said: "While the full details of this horrific murder are still emerging, testimony from journalists who were with her when she was killed point towards this being another deliberate and systematic targeting of a journalist. Yet again journalists, wearing press vests, clearly identified were targeted by Israeli snipers. They were not alongside demonstrators, they were not a threat - they have been targeted to prevent them bearing witness and telling the truth about the Israeli action in Jenin.
"We will seek to add this case to the ICC complaint submitted by the IFJ, detailing such systematic targeting. If we demand justice for the Russian targeting of Ukrainian journalists we must demand an end to, and justice for, Israeli targeting and killings of Palestinian journalists".