It's getting tougher for a company to pull out of trouble once the auditor expresses doubt in an audit opinion about whether the company can remain in business, according to the latest data on going-concern qualifications.

In its analysis of more than a decade of going concern filings, Audit Analytics found only 140 companies filed a clean audit opinion in 2012 after getting a red flag from auditors the year before. It's the first time the number dipped below 200 since 2000. In the two prior years, the number fell from 277 to 207 before hitting its low of 140 in 2011.

Based on more than 90 percent of filings submitted so far in 2013, Audit Analytics is predicting 2,517 companies will ultimately carrying the going concern qualification on their audit opinions when all 2012 financial statements are filed. That's 127 fewer companies than the 2644 reported in 2011, and the fourth consecutive year the number fell from a high of 3,352 in 2008.

Although the number of going concern filings fell for the fourth straight year, it doesn't necessarily mean company performance has improved, according to the research firm analysis. A certain number of companies will naturally fall off the list because they won't recover from whatever downfall led to the going concern qualification and therefore won't file financial statements in the subsequent year, the firm says. Based on its analysis of prior year data, Audit Analytics says 228 companies will drop out of capital markets for that reason, yet the decline is only 127.

The research data also shows that going concern qualifications have been handed out to a higher percentage of companies in the past six years than in the six years prior to the ramp up to the financial crisis. From 2000 to 2006, the percentage of companies that drew the going concern warning ranged from 14.1 percent in 2006 to a high of 17.4 percent in 2006. Then the climb began in 2007 when the percentage rose to 19.9 percent, peaked in 2008 at 21.1 percent, and tapered to 17.7 percent in 2011 and 17.5 percent in 2012.