"I am not vetting my V.P. search committee for their mortgages," Obama said Tuesday.
He accepted Johnson's resignation on Wednesday, leaving the search at least temporarily in the hands of two other prominent Democratic attorneys who also had been scouting candidates - former Deputy Attorney General Eric Holder and Caroline Kennedy.
"Jim 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. "We have a very good selection process under way, and I am confident that it will produce a number of highly qualified candidates for me to choose from in the weeks ahead."
Johnson, the former chairman of mortgage lender Fannie Mae, came under fire from GOP candidate John McCain and the Republican Party after The Wall Street Journal reported last Saturday that Johnson got mortgages with help from the CEO of Countrywide Financial Corp.
McCain had accused Obama of hypocrisy for speaking out against Countrywide's role in the subprime mortgage crisis.
Obama's campaign declined to say whether he would replace Johnson, who also led the vice presidential search effort for Democratic nominee John Kerry in 2004 and Walter Mondale in 1984.
Obama said he was grateful for Johnson's service.
Johnson's resignation may allow Obama to move ahead with the search process without the criticism surrounding him, but it also could make it appear that the campaign quickly caved under pressure. The resignation touched off a series of accusations between the two campaigns about which candidate has more tainted advisers and better judgment about who to surround himself with.
Obama's campaign has had varying responses when controversy has focused on those around him. Foreign policy adviser Samantha Power left within hours of calling Hillary Rodham Clinton a "monster."
Obama was initially reluctant to disavow his pastor, Jeremiah Wright, after video of racially explosive sermons emerged. And he kept leading economic adviser Austan Goolsbee on board amid controversy surrounding his private comments on free trade.
At least five McCain staffers have left his campaign after a Democratic uproar over McCain's connections to lobbyists. McCain responded by banning registered lobbyists serving his campaign but has defended two of his top advisers - Rick Davis and Charlie Black - who left their lobbying jobs to work for his presidential bid.
Johnson and Holder held meetings this week with lawmakers on Capitol Hill to seek their input on possible running mate candidates.
Obama said Tuesday that Johnson had a "discrete task" and was performing it well. He suggested the Countrywide connection was not a problem since Johnson was an unpaid volunteer and hadn't been assigned to work in a future administration.
Kerry, a prominent Obama supporter, told reporters earlier Wednesday that Johnson had done an outstanding job of gathering information for him four years ago and keeping it private. He declined to say whether he'd recommended that Obama keep Johnson on amid the controversy.
