Testifying before the Senate Intelligence Committee, National Intelligence Director James Clapper said he meant last week only that the group is trying to work within secular politics, CNN reported.
Committee Chairwoman Dianne Feinstein, D-Calif., questioned Clapper on the Brotherhood's stances on Arab-Israeli peace, Iran and smuggling weapons into Gaza.
Clapper said the facts are murky, but he would assume the group opposes Egypt's peace treaty with Israel and favors shipping arms Gaza, which is ruled by its ally Hamas. He added there are internal differences.
Feinstein also asked whether spy agencies had spotted enough clues in social media before the Arab uprisings.
Clapper defended the U.S. government's Open Source Center's record in monitoring all media.
CIA Director Leon Panetta, who also testified, said it is an enormous task to track the hundreds of thousands of Facebook accounts, millions of tweets and hours of YouTube video daily.