James Johnson "did not want to distract in any way from the very important task of gathering information about my vice presidential nominee, so he has made a decision to step aside that I accept," Obama said in a statement.
Johnson said he did nothing improper but was resigning so he would not be a liability, The Washington Post reported.
"I would not dream of being a party to distracting attention from that historic effort," Johnson said in a statement, a portion of which was on ABC News' Web site. "I believe Barack Obama's candidacy for president of the United States is the most exciting and important of my lifetime."
The Wall Street Journal reported Saturday that Johnson, a powerful Democratic Party insider and former chief executive of Fannie Mae, got personal loans at favorable rates from embattled Countywide chief executive Angelo Mozilo.
Johnson was one of three people on Obama's search team, which includes Deputy U.S. Attorney General Eric Holder and Caroline Kennedy, daughter of President John Kennedy. A replacement has not been announced.