The new transcript of Catherine Ashton's remarks mentions the situation of children in both Gaza and the southern Israeli town of Sderot after the first version only mentioned the Palestinian territory.
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A video of her speech Monday showed she indeed mentioned Sderot, a town often hit by Palestinian rocket attacks.
After a day filled with criticism from Israeli officials including Prime Minister Benjamin Netanyahu, Ashton denied that she ever compared the shooting at a Jewish school in Toulouse and the situation in the Middle East.
"I am really saddened by the distortion of my remarks," she told the EU parliament's foreign affairs committee. "I drew no parallel whatsoever between this tragedy and events elsewhere in the Middle East.
"I condemn unreservedly the terrible murders at the Ozar Hatorah school in Toulouse yesterday and extend my sympathies to the families and friends of the victims, to the people of France and the Jewish community."
In her speech at a youth event, Ashton paid tribute to children killed in "terrible circumstances" and listed a number of tragedies including unrest in Syria, last year's Norway massacre and the Toulouse shooting.
"When we see what is happening in Gaza and Sderot, in different parts of the world -- we remember young people and children who lose their lives."
The phrase "and Sderot" had been missing from the first transcript of the speech given at the event in Brussels organised by the UN relief agency for Palestinian refugees (UNWRA).
The new text was released after a day of damage control, with her spokesman Michael Mann insisting her remarks were "grossly distorted," although he had not indicated at the time that she had talked about Sderot too.
Mann added that Ashton was making a "general remark" about violence against children around the world.
"She wanted to draw attention to the unfortunate fate of children around the world who lose their lives. Any indication or suggestion that there is a comparison or a parallel is incorrect," he told reporters.
EU officials contacted Israeli counterparts to clarify Ashton's remarks, an EU diplomat said.
Before the new transcript was released, Netanyahu, his defence minister and his foreign minister all criticised the remarks.
"What especially outrages me is the comparison between a targeted massacre of children and the surgical defensive actions of the IDF (Israel Defence Forces), intended to strike at terrorists using children as human shields," Netanyahu said.
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