The new divisions are Land & Naval and R&D and Engineering.
A new business sector has also been created -- Air & C4ISR Systems, which will include air-to-ground systems, electro-optical systems, communications and intelligence.
"These changes were made in keeping with our vision to serve as a significant pillar in Israel's security, in addition to serving as its National Laboratory, while maintaining our robust financial performance, with sales of over $1.7 billion in 2012, and an order backlog covering more than two years," said Yedidia Yaari, Rafael president and chief executive.
"We pride ourselves on our superb scientists and engineers, who since Rafael's establishment have developed some of the world's most ground-breaking systems, such as Iron dome, TROPHY, Protector, and many others.
"I am happy to say that we are continuing to constantly and consistently recruit more such excellent personnel to our ranks. I am convinced that these changes will serve us in achieving our plans and goals and in meeting our future challenges," he said.
Other organizational changes include the company's Air Defense Directorate becoming the Air superiority Systems Sector, responsible for air and missiles defense systems.