Deloitte & Touche LLP has resigned as the auditor for American Apparel and has been replaced with the troubled garment retailer’s former auditor Marcum LLP.

Deloitte had served as American Apparel’s independent registered public accounting firm since April 3, 2009, but had warned the company and its CEO Dov Charney back in March of material weaknesses in the company’s internal control environment, and in the financial closing and reporting process.

Deloitte noted at the time that the company did not have enough adequately trained accounting personnel in its foreign subsidiaries with expertise in GAAP and it also found problems with the accounting for inventory. Some of the merchandise inventory costs also were not accurately analyzed and recorded by the company’s foreign subsidiaries.

In its latest filing, the apparel company insisted that it had no disagreements with Deloitte on accounting principles or practices, and there were no “reportable events” aside from the material weaknesses found in the March report on the company’s 2009 financials.

However, American Apparel noted, “Deloitte advised the Company that certain information has come to Deloitte’s attention, that if further investigated may materially impact the reliability of either its previously issued audit report or the underlying consolidated financial statements for the year ended December 31, 2009 included in the Company’s 2009 Form 10-K. Deloitte has requested that the Company provide Deloitte with the additional information Deloitte believes is necessary to review before the Company and Deloitte can reach any conclusions as to the reliability of the previously issued consolidated financial statements for the year ended December 31, 2009 and auditors’ report thereon.”

The audit committee of American Apparel’s board discussed the matters with Deloitte, and the company authorized Deloitte to respond fully to the inquiries of the successor accountants at Marcum concerning each of the matters. Marcum had earlier expressed an adverse opinion on American Apparel’s internal control over financial reporting for 2008 before it was terminated in April 2009. The change of auditors has delayed the company’s financial filings in the past, and its stock nosedived 25 percent after news of the latest change of auditors was announced on Thursday.