Brown, 52, has been in the Massachusetts Guard for 33 years and was promoted to colonel in November. His new assignment is in the Pentagon, as assistant to Col. Christian Rofrano, chief counsel of the National Guard Bureau, The Boston Globe reported.
He said he transferred a few weeks ago.
"I didn't want to politicize my record,'' Brown said. "I wanted to go to a place where I would be treated on the merits. ... I didn't want any reference that Scott got special preference.''
Brown denied that he left the Massachusetts Guard because there were no available postings for a colonel in the Judge Advocate General's Corps, where he has served since 1994.
Brown's military record has been under scrutiny as he campaigns for a full term in the Senate. He won a special election to succeed the late Edward Kennedy, winning a seat that had been held by Democrats since John F. Kennedy took office in 1953 and becoming the first Republican to represent Massachusetts in the Senate since 1979.
Brown is expected to face a stiff challenge from Elizabeth Warren, the likely Democratic candidate.