Al-Arabiya's Atwar Bahjat and two colleagues from the local Wassan media company, engineer Adnan Khairullah and cameraman Khalid Mahmoud, were in the city to cover the bombing on Wednesday of a revered Shia shrine.
Their employers lost contact with them on Wednesday night.
Their bullet-riddled bodies were found on Thursday morning near their vehicle, cameras and satellite dish on the outskirts of the city, 95km north of Baghdad, police Captain Laith Muhammad said.
The office of Jalal Talabani, the Iraqi president, called the killing "a criminal and cowardly act" in a statement that praised Bahjat and her colleagues as professional journalists who "never stopped defending the truth".
When a reporter asked Talabani during a news conference to allow journalists to carry weapons to defend themselves, he said: "Send me an official request and I will approve it and inform concerned agencies to give you the right to carry arms."
Ibrahim al-Jaafari, the Iraqi prime minister, ordered security authorities to find the killers of the three journalists and bring them to justice.
The three journalists had been reporting live on Wednesday from the edge of Samarra, which was sealed off by security forces after the early morning explosion at the Askariya shrine, also known as the Golden Mosque.
Bahjat's last broadcast was at 6pm (1500 GMT), Al-Arabiya said.
The team was preparing to return to Kirkuk when two gunmen pulled up in pickup truck, shooting in the air and shouting: "We want the correspondent," according to a cameraman who evaded capture, Al-Arabiya reported.
The three were taken away, and their bodies were found about 10km northeast of Samarra, police and Al-Arabiya said.
Press freedom group Reporters Without Borders expressed horror at the killings.
"We will never stop repeating that journalists are neutral and vital observers," the group said in a statement. "They are neither combatants nor targets to be shot down. Their work must be protected and respected, whatever their nationality and regardless of which media they work for."
A total of 82 journalists and media assistants have been killed since the start of the Iraq war in March 2003, including seven this year, according to a Reporters Without Borders Count.
Bahjat, who left Aljazeera in December to join Al-Arabiya, was the seventh woman journalist killed.