Bill Gross and Larry Fink manage a $3 trillion pile of bonds—an amount almost as big as Germany's economy. Their firms, Pacific Investment Management Co. (Pimco) and BlackRock Inc., doubled holdings since 2008, outpacing the market's growth of 50 percent.

Some of the largest hedge-fund firms, including Bridgewater Associates LP and BlueCrest Capital Management LLP, have also more than doubled their investments in debt, data compiled by Bloomberg show. At the same time, Wall Street banks are shrinking their stakes in bonds, Federal Reserve data show.

The lopsided bond market has caught the attention of the U.S. Securities and Exchange Commission. Not only is the SEC examining whether the biggest players get preferential prices and access because of their influence, it's also worried about what happens when the five-year bond rally ends as U.S. policy makers prepare to raise interest rates.