Should Kansas Athletic Director Lew Perkins receive his first retention bonus of $2.05 million on June 30, the clock begins on another tax-free payment for Perkins.

According to amendments to Perkins’ contract provided by Kansas University, if Perkins stays with the university from July 1 through June 30, 2013, he would receive another $1.2 million from Kansas Athletics.

Perkins would be paid $600,000 if he stays through June 30, 2011, and an additional $600,000 for staying through June 2013. As with the first retention bonus, all money used would come from Kansas Athletics funds with no state taxpayer dollars involved.

Lynn Bretz, a KU spokeswoman, said retention agreements were not uncommon in athletics, and reflected a desire to ensure Perkins remained on as athletic director. She highlighted several accomplishments during his tenure, including a 2.99 fall 2008 grade-point average for all student-athletes in KU’s 18 sports programs, which represented an athletic department record for a fall semester.

Also, several of the sports programs have achieved postseason success, including conference titles, two consecutive bowl victories for football and a men’s basketball national title.

Kansas Athletics will be on the hook for more than $1.5 million to cover Perkins’ personal income taxes in addition to his upcoming $2.05 million bonus, according to estimates from a certified public accountant.

Using a formula outlined in his contract and taking into account Perkins’ current salary and existing tax rates, Kansas University would write Perkins a $3.59 million check in gross earnings from athletics funds so that he can take home $2.05 million in net bonus pay, according to an estimate from Randy Renfro, a CPA with Roark & Associates, PA, who agreed to assist the Lawrence Journal-World with the calculation.

A similar calculation would be done on the next retention payments using the tax rates from that particular year, according to the agreement negotiating the payments. That document was signed by Perkins on March 25, 2008, and Chancellor Robert Hemenway on April 12, 2008.

Perkins makes an annual salary of $800,000 plus an additional $100,000 for media relations work. Bretz said that work included engaging in public relations efforts, meeting with the media, making news announcements and appearing at recognition and other ceremonies and at sporting events.

The $800,000 salary was raised in July 2008. When he was originally hired, it was $400,000.

“In essence, Lew’s salary was changed to reflect unparalleled excellence on many fronts,” Bretz said.

As part of renegotiating Perkins’ salary, a previous portion of Perkins’ contract allowing him a $75,000 annual performance bonus if Perkins met certain criteria was removed.

KU pays a part of Perkins’ salary through state funds to support institutional control. In the current fiscal year, $194,011 of his salary is paid using state funds. The balance comes from Kansas Athletics funds.

Additional documents provided by KU on Wednesday afternoon showed that Perkins’ employment contract at KU had been extended by two years, through June 2015.