"Im ready to admit that we never expected to face such opposition against the deal, in particular not in Berlin," Enders said in a letter to employees obtained by AFP.
Enders noted the "strong efforts by the French and UK governments" to overcome what proved to be "insurmountable" political hurdles facing a tie-up that would have created a €35 billion ($45 billion) aerospace giant.
For Enders, the merger was the "logical, long-overdue step in the European integration of our industry" and that the ill-fated move was true to the company's longterm strategy plan, known as Vision 2000.
Enders said the company would now "take the time to clearly draw a number of lessons from this experience" including a "review of our Group strategy and defence activities in particular."
"If anything, our relationship (with BAE) has been strengthened through this endeavour," he said.
"This is an excellent basis for the further development of our business ties in the defence field."
A merger to create the biggest aerospace group in the world between EADS and BAE Systems collapsed on Wednesday, with analysts saying Germany shot it down because the country feared it would be sidelined.
But German Defence Minister Thomas de Maiziere denied the collapse was Germany's fault.