The company has hired an external company called FTI to assist with finances, and an internal audit is addressing money owed.
He said though the company's reputation has been damaged, oil companies continue to work closely with Pilot and the company is assuring customers they will continue to have the same high supply of fuel.
Pilot business is down one and a half percent following the FBI raid, Haslam said, but he blames that on a shrinking market.
He also said there was a large amount of confusion after the April 15 raid, and the affidavit revealed only the "potential for wrong-doing."
Many trucking companies at the seminar said they're still doing business with Pilot and have no plans to stop.
"We buy the majority of our fuel from their company. We have a good relationship with them," said PGT Trucking Chief Financial Officer David Henry.
"Jimmy's doing all the right things, saying the right things, as he should," said Bestway Express President & CEO Shepard Dunn.
But it was clear some members of the trucking industry are still skeptical.
President of the American Trucking Association Bill Graves asked Haslam questions that were submitted by different trucking companies who are looking for answers.
"There are several suggestions in the federal affidavit that you personally were aware of the scheme to underpay rebates to some of your customers. Were you and did you participate in any way?" he asked the Pilot Flying J CEO and president.
"Absolutely not," Haslam replied.
Graves said the trucking industry is looking to make all potentially cheated companies whole again and to bring any Pilot Flying J employee to justice if they did, in fact, intentionally defraud their customers.
"We're in the wait and see mode. Do they actually make good on all those promises?" Graves wondered.
During his address, Haslam said Pilot hasn't had many issues with creditors, saying the company is still working well with banks and even oil companies despite the investigation.