Claudia Ruiz Massieu flew out of Mexico late yesterday vowing to seek answers on the attack that killed 12 people, including at least two Mexicans. Six other Mexicans are still unaccounted for.
Egypt said the tourists entered a restricted area in the vast Western Desert and were "mistakenly" killed while security forces chased jihadists who had abducted and beheaded an Egyptian they said worked for the army.
Ruiz Massieu said six Mexican survivors told their ambassador they had "suffered an aerial attack with bombs launched by a plane and helicopters" after stopping for a roadside lunch.
"We face a terrible loss of human lives and an unjustified attack that obligates us to make the protection of our citizens the priority," Ruiz Massieu said before departing Mexico with relatives of those killed and doctors.
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She said she would talk to top Egyptian officials to "clear up the circumstances of this deplorable event, which has cost the lives of innocent Mexican tourists".
The incident has proven embarrassing to the Egyptian security forces which regularly claim to have killed dozens of militants in air strikes, tolls that are difficult to independently verify.
The State Department said US embassy staff were checking "reports of a potential US citizen involved," without elaborating.
Hassan al-Nahla, the head of the union for tour guides in Egypt, said the tourist group had received all the required permits and set off with a police escort from Cairo to Bahariya oasis, roughly 350 kilometres (220 miles).
About 80 kilometres from their hotel, they veered two kilometres into the desert to have lunch after one tourist said she suffered low blood sugar and needed food, he said in a statement.
"I don't blame anyone but I ask who is responsible for coordination, and why was it absent?"
Ruiz Massieu said she would enquire about the matter.