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Stung by criticism his agency is mismanaged, HART’s executive director continued a vigorous defense in a written response accompanying the final version of an audit released Friday.

In an 85-page response, Dan Grabauskas defended his beleaguered agency by continuing to attack City Auditor Edwin Young, accusing him of improprieties and irregularities during the audit and suggesting that proper auditing standards were not followed.

“As an organization, HART welcomes critical, vigorous and healthy oversight,” Grabauskas wrote. “Accordingly, it is discouraging when a report is written in a fashion to intentionally mislead, is issued in an improper manner, and conceded to politically motivated pressure.”

He wrote that HART had received a draft copy of the report six weeks ago and found it to contain “factual errors, misleading statements and unsupported conclusions.” But the final audit didn’t include “comments and clarifications” HART wanted to see.

Grabauskas’ response in the final audit was toned down somewhat from his statements at a hastily called press conference Thursday when he accused City Auditor Edwin Young of leaking a draft version of the audit, which had been circulating among city departments for more than a month, and characterized the report as a “joke” and a “mess.”

The is nearly identical to a draft that was leaked to the media Thursday. It takes HART to task for management shortcomings that raise questions about whether it could control costs on the largest public works project in state history.

In his full written response, which wasn’t included in the draft audit report, Grabauskas disagreed with most of the audit’s recommendations. And in a 62-page attachment to a 23-page letter, he addressed each section of the report with detailed explanations supporting the agency’s position.

He said in some cases the auditor’s staff was unable to understand highly complex engineering documents and did not have the professional expertise to understand what was going on.

HART itself has had to buy its expertise, spending hundreds of millions on consultants to perform design and engineering services and tens of millions more for consultants to manage the construction activities.

Among HART’s specific responses:

• The agency challenged the recommendation that it more consistently provide reliable cost information, saying that it currently provides that information to public officials, the HART Board of Directors, federal authorities and taxpayers by publishing it in HART’s Monthly Progress Report.

• HART rejected the recommendation that it should document details and provide supporting information for its cost estimates, saying that “every estimate produced in the recent past and for the remainder of the project will be accompanied by a Basis of Estimate report outlining assumptions and methodologies.”

HART didn’t say whether it intended to publicly release the estimate reports.

• Regarding the audit’s findings that HART’s financial and operating plans are out of date and unreliable, the rail agency said it is revising its financial plan to account for a General Excise Tax surcharge extension, but it blamed revenue shortfalls and cost overruns on “external factors beyond anything under HART’s control.”

In a cover letter accompanying the final audit report, Young told City Council Chairman Ernest Martin that the auditor’s office had nothing to do with a draft audit report being leaked, saying distribution of the confidential drafts had been limited solely to authorized city and HART officials.

“HART requested and received early distribution of the drafts and conceded it distributed the confidential drafts within its organization without our permission,” Young said, adding that “HART’s attempts to discredit the audit work and attempts to intimidate the auditors were unprofessional.”

Here’s the final audit report: