The California-based mortgage lender, which was taken over by the government last month after its capital ratios became dangerously low, is to modify the loans in a bid to limit foreclosure numbers and boost revenue.
According to the Federal Deposit Insurance Corporation (FDIC), who helped to draw up the plan, the new loan strategy will also help IndyMac pay back its own creditors more quickly.
FDIC chairman Sheila Bair said: "This is a well balanced program that will maximize the value of these loans, ultimately returning more money to uninsured depositors and creditors, along with investors in the servicing portfolio.
"At the same time, we hope to keep tens of thousands of troubled borrowers in their homes and avoid the negative consequences that foreclosures can have on the broader economy."
Under the terms of the plan, interest rates for most borrowers who are currently in default will be capped at 6.5 per cent.