David Goldman for The New York Times

MF Global improperly diverted customers’ cash for its own use in the days before its bankruptcy, an act that regulators believe may help explain why $600 million of customer funds remains missing, people briefed on the investigation say.

Investigators have now zeroed in on hundreds of millions of dollars in suspect borrowing at the commodities and derivatives brokerage firm, which at the time of its collapse was run by Jon S. Corzine, the former Democratic governor of New Jersey. At least some of that money was used to cover trading losses at MF Global, regulators suspect, meaning the money may no longer be simply missing. It may be gone.

MF Global, like other brokers, can use customer cash if it puts up sufficient collateral. But the firm did not provide enough backing in late October, essentially taking free loans, said the people briefed on the investigation, who spoke on the condition of anonymity because the inquiry was continuing.

As customers rushed to withdraw money while the firm was teetering on the brink of bankruptcy, that questionable borrowing worsened a liquidity crisis at the firm.

It is unclear what MF Global did with all of the money or whether it can be recovered. The firm may have used some of the cash to keep its own lenders at bay, which means the money could be sitting in an account at another firm.

And some of the $600 million may yet materialize. As a patchwork of federal agencies and the trustee overseeing the firm’s liquidation reconstruct MF Global’s books, they expect to find that in the chaotic last days the firm failed to record when some customers received their money.

But a big chunk will most likely be much harder to recover, the people say, because it was used to pay off losses, rather than back trades.

The search for the missing money has touched the breadth of the commodities futures business, from Wall Street hedge funds to Midwest farmers. As hundreds of examiners pore over records around the clock, comb through 38,000 customer accounts and interview former employees, brief moments of hope have emerged only to later be proved false.

An MF Global spokesman declined to comment. Neither the firm nor Mr. Corzine have been accused of wrongdoing.

A lawyer for MF Global, Marc E. Kasowitz, said the company and its employees were cooperating with regulators as well as the trustee.

“Any characterization at this point of what occurred at MF Global is premature and inappropriate,” Mr. Kasowitz said in a statement.

The failure of the brokerage firm set off a wave of panic among its tens of thousands of customers. Many of them are farmers and small-business owners, who use these markets to protect themselves from swings in the prices of crops and metals.

In a federal bankruptcy court hearing in Lower Manhattan on Thursday morning, a federal judge approved the transfer of about 60 percent of the cash-only accounts sitting at MF Global to its 23,000 rightful owners, totaling about $520 million. The trustee, James W. Giddens, plans to begin dispersing the money before Thanksgiving.

The missing money strikes at the very heart of the futures industry. Brokerage houses and traders have long depended on the promise that customer cash will be kept separate from the firm’s money. This ensured that even if the firm were on the cusp of collapse, customers could safely access their money.

To unravel the mystery, the federal government has dispatched an assortment of regulators and criminal investigators. The Commodity Futures Trading Commission is leading the search for the missing money.

Investigators believe that money was transferred from the futures business to its securities brokerage division, according to people with knowledge of the inquiry. The Securities and Exchange Commission is helping to trace where that money went. The Federal Bureau of Investigation, meanwhile, is examining potential criminal wrongdoing, and the United States attorney’s offices in Chicago and Manhattan have issued subpoenas in the matter.

Of interest to authorities are these two main businesses run by MF Global. The futures side of the operation traded contracts for wheat, corn and metals. That is where the customer money went missing. The other side, which focused on securities, was where the firm placed a $6.3 billion bet on the sovereign debt of five European countries. Those wagers alarmed investors when they were disclosed, prompting a crisis of confidence that led to the firm’s demise.

On Oct. 24, Moody’s Investors Service lowered its credit rating on MF Global, citing concerns about its European debt exposure. Trading partners began demanding more collateral.

MF Global held a fire sale that week, reducing its assets to $23 billion from $55 billion, according to a person with knowledge of the matter. But the flood of requests kept coming from both customers and trading partners, and MF Global began to shift money to its securities division.

Like many futures shops, MF Global routinely borrowed money from customers and replaced it with assets like United States Treasury securities. Firms often keep a cushion of cash to protect customer funds, which they are allowed to tap with certain restrictions.

But according to the people briefed on the investigation, MF Global depleted this buffer and then dipped into the customer accounts to the tune of hundreds of millions of dollars. And in the days before the collapse, the firm stopped backing the loans it took from customers.

It is unclear whether MF Global officials knowingly used customer money or if they believed the buffer was intact. If investigators determine that MF Global intentionally tapped the customer funds, they could file both civil and criminal charges.

MF Global’s customers who acted fast got their money back. The rest now must wait in line, and may never fully recover their funds. Bankruptcy experts doubt the trustee will be able to claw back money secured by clients who rushed out the door.

The process will almost certainly be painful. The trustee has transferred some money backing open trades from MF Global to other brokers. And soon, the trustee will begin the transfer of 60 percent of cash accounts back to its owners.

But as proof of how complex and messy these affairs can be, customers with cash as well as open trades do not yet qualify to get any of their cash back.

Jason Skole, an investor in Boca Raton, Fla., had about $200,000 trapped at MF Global when the firm filed for bankruptcy, a fraction in open trades and the majority in cash.

“You don’t worry about any insurance in this industry because your money is protected, but it’s not,” Mr. Skole said. “It’s a terrible situation. It’s doesn’t make for a good Thanksgiving or Christmas.”