President Obama’s second term will almost certainly mean deep cuts in military spending that could lead to job losses in the state’s multibillion dollar defense sector that includes one of Massachusetts largest employers, Raytheon Co.

While Mitt Romney pledged to bulk up the Navy, Obama has long advocated for leaner armed forces. “Obama’s priorities for the years ahead spell trouble for the Massachusetts defense industry,” said Loren Thompson, a defense analyst at the Lexington Institute in Washington, D.C.