Pay raises and promotions were improperly given to some employees of the Delaware River Port Authority in recent years, according to an audit by the DRPA's inspector general.

Thomas W. Raftery III faulted the agency's chief executive officer, John Matheussen, for giving selective raises without following agency rules or getting proper approval from DRPA board leaders.

Matheussen disputed Raftery's findings, along with the DRPA's chief administrative officer and director of human resources, in a lengthy rebuttal, challenging the audit as "flawed," "not based on fact," and "misleading."

The audit said Matheussen gave large raises last year to two electrical foremen for PATCO, the commuter rail line operated by DRPA. That prompted "me-too" raises to the same salary of $79,500 for 26 other DRPA and PATCO foremen.

The audit said Matheussen did not get advance approval from the board chairman or vice chairman for the raises. A 2003 DRPA provision requires such approval for all raises greater than 8 percent, Raftery said.

Raftery cited 337 raises exceeding the 8 percent threshold since 2007.

Raftery also chastised the DRPA for a lack of consistency and procedures for raises and promotions, which he said created low morale among employees, most of whom have not received raises for five years.

The pay-raise audit, which was completed in May and released last week, comes amid tensions between Raftery and Matheussen as well as some board members.

Raftery, a former FBI agent, was hired as the DRPA's first inspector general in January 2012, to serve as its financial and ethical watchdog.

He has been at odds with Matheussen over several issues, including his insistence that he report to the board and not Matheussen on his investigations. New Jersey board members on the bistate agency have balked at efforts to establish operating standards for Raftery's office and blocked an effort last year to raise his salary from $130,000 a year to $165,000.

In June, DRPA Board Chairman David Simon publicly announced some of the findings of several unreleased Raftery audits, prompting complaints from Matheussen and Vice Chairman Jeff Nash, who said the reports should not be publicly discussed until staff responses were prepared.

The pay-raise audit was one of those.

Last month, William Sasso, one of the Pennsylvania board members, criticized Raftery in a board committee meeting, accusing him of manipulating facts to suit his conclusions.

Raftery responded that "this process is getting pretty old . . . the bickering and the questioning of my integrity."

"If you do not want me to ask employees questions, then you should get rid of my position. You have to decide whether or not you want an inspector general here."

The latest audit can be viewed at www.drpa.org/drpa/inspector_reports.asp.

Contact Paul Nussbaum at 215-854-4587 or pnussbaum@phillynews.com.