As the company battles those accusations, industry participants say it has once again been moving to capture business by offering Wall Street underwriters higher ratings than other agencies will offer. And it has apparently worked. Banks have shown a new willingness to hire S.& P. to rate their bonds, tripling its market share in the first half of 2013. Its biggest rivals have been much less likely to give higher ratings.
"The general consensus was that these changes have let them get their market share back," said Darrell Wheeler, a bond analyst at Amherst Securities.
Standard & Poor's said the "methodology used and the conclusions drawn by The New York Times are flawed," though it declined to elaborate on what those flaws were.
In its response to the government lawsuit, the company said that its ratings had always been "uninfluenced by conflicts of interest."
But David Jacob, who ran the S.& P. division that rated mortgage-backed bonds until 2011, said that in his time at the company, after the financial crisis, he saw employees adjusting criteria in response to business pressure.
"It's silly to say that the market share doesn't matter," said Mr. Jacob, who is now retired. "This is not God's holy work. It's a business."
Along with its chief rivals — Moody's Investors Service and Fitch — S.& P. was criticized for offering top-flight ratings to subprime mortgage securities, which made those bonds appear more attractive to investors before the crisis. The agencies had an incentive to offer higher ratings because banks choose which ratings agency grades each bond. The flaws in the system became apparent when many bonds with the highest ratings ended up plunging in value, inflicting enormous damage on the economy.
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The government, though, chose in February to file suit against only S.& P., accusing it of relaxing its rating methodology before the crisis to win business.
The methodology and motivation of the ratings agencies are important because they play such a vital role in the financial system. Many investors are allowed to buy only bonds that have been rated AAA by S.& P. or one its two largest competitors, Moody's and Fitch. Banks often adjust the riskiness of their investment products to satisfy the agencies.
But the agencies have long been accused of tailoring their ratings to the banks to win more business. Before the crisis, the biggest problems involved ratings of bonds tied to subprime residential mortgages. More recent concerns have come about since S.& P. made an apparently benign change last September to the criteria it uses to rate bonds backed by commercial real estate mortgages, which is now the hottest portion of the mortgage bond market.
The company said at the time that the change was not designed to win more business. Before the change, though, S.& P. was lagging, in part because of tougher standards it put in place immediately after the crisis.
Since the change, the company has been much more likely than its big rivals to offer higher ratings on the commercial real estate bonds, according to the analysis for The Times. On half of the deals that it rated since last September, S.& P. has given at least a portion of the deal a higher rating than the other agencies rating the same deals. Before the change in standards, it rarely offered higher ratings.
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Some investors buying the bonds worry that the willingness of some agencies to give better ratings is encouraging banks to issue lower-quality bonds.
"When one agency loosens up on something, it forces others to as well," said Edward Shugrue, the chief executive of the bond investing firm Talmage.
Immediately after the crisis, the agencies themselves moved to tighten their standards. S.& P. offered top positions to Mr. Jacob and his partner, Mark Adelson, from the consulting firm Adelson & Jacob, both of whom had called for more scrutiny of bonds.
The two quickly pushed inside the company for tougher standards for the bonds that were at the root of the financial crisis. This alienated many banks, and the agency was rarely chosen to rate the mortgage-backed bonds. The company rated only 22 percent of the bonds issued in 2011, down from 80 percent in 2006.