The station's Baghdad bureau was attacked by United States aircraft just two weeks after David Blunkett advised Tony Blair, the British prime minister, that Al Jazeera's television transmitter in the Iraqi capital should be bombed.
"Al Jazeera Network is outraged at such an attitude toward the free press," a statement said.
"As an international news organisation, Al Jazeera Network is obliged by law to address its employees' increasing concerns for their very lives".
Tareq Ayoub, an Aljazeera reporter, was killed during the US bombing in April 2003.
In Monday's interview, Blunkett, who was a member of Blair's war cabinet at the time during the 2003 invasion, said he had advised the prime minister that he considered Al Jazeera's Iraq technical operation to be a legitimate target.
"There wasn't a worry from me because I believed that this was a war and in a war you wouldn't allow the broadcasts to continue taking place," he said the interview with Britain's Channel 4 television.
When he was asked whether attacking a media outlet was not against international law, he said: "Well I don't think for a minute in previous wars we'd have thought twice about ensuring that a propaganda mechanism on the soil of the country you were invading would actually continue being able to propagandise against you".
"I don't know whether it was a mistake or not, but I wouldn't call it legitimacy," Blunkett said of the bombing.
Al Jazeera has urged Blair to make an official response to the interview.
"We find Mr Blunkett's allegations and position to be irresponsible and dangerous not only for Al Jazeera but for the freedom of media everywhere in the world," the station added.
Ahmed al-Sheikh, editor-in-chief of Al Jazeera's Arabic channel, said; "Al Jazeera was being targeted at the time because the people who were waging war on Iraq didn't like what it was showing.
"We talk about terrorism, this [was] pure terrorism."
He said Al Jazeera had broadcast the realities of the war on the ground while other media outlets were covering "the cosmetics".
The Qatar-based channel was repeatedly criticised by US officials during the 2003 invasion of Iraq who accused it of bias but it also came under fire from Saddam Hussein's regime who banned two of its reporters from broadcasting.