He said reports of the relationship between Smith and MedBest "raised significant red flags about this company's contracts with the state."
MedBest said nobody was available Friday to comment.
Smith said in a statement Thursday he is cooperating with SUNY's probe and will resign "to avoid further distraction for the University from its important mission."
SUNY Chancellor Nancy Zimpher told Smith in a Nov. 1 letter to give up any claim to a $350,000 deferred compensation plan from MedBest, provide a full accounting of all pay he has received since taking over as president in 2006 and warned it is likely he will have to make "substantial repayments." The letter was obtained by the Albany Times Union.
Zimpher said the review will also include "a substantial increase in your compensation in 2012 (continuing into 2013) paid through the Pediatrics Service Group LLP without my prior approval."
Pediatrics Service Group is the partnership of pediatricians on the medical school faculty who provide care at Upstate Golisano Children's Hospital. It said in a statement Friday that it brought "concerns about the compensation arrangements" to SUNY and is helping with the review.
SUNY spokesman David Doyle said Friday the probe is being expedited, but there is no timetable for its conclusion. He said Smith hadn't yet formally resigned.
Before joining SUNY, Smith had been chancellor of Texas Tech University, president of the Texas Tech University Health Sciences Center and dean of the School of Medicine and Graduate School of Biomedical Sciences, according to SUNY's website. In the mid-1990s, Smith was commissioner of the Texas Department of Health.