The penalty is the largest fine levied in the five-year history of California's Department of Managed Health Care, said agency spokeswoman Lynne Randolph.
Oakland-based Kaiser held the previous record of $1 million, imposed in 2002 for the HMO's care of a Northern California woman who died.
A Kaiser spokesman didn't immediately return a message seeking comment.
Kaiser suspended its Northern California kidney transplant program in May amid mounting regulatory pressure and patient lawsuits alleging that botched paperwork and administrative errors had imperiled patients' lives.
Problems arose when Kaiser ordered Northern California kidney patients to transfer from University of California hospitals to its new transplant center in 2004.
Kaiser failed to discuss with regulators the transfer of up to 1,500 patients to the new center, delaying some patients' procedures, the Los Angeles Times reported. Only 56 transplants were performed at the Kaiser's San Francisco center in 2005, while twice that number of people died waiting for a kidney, the Times reported. At other California transplant centers, more than twice as many people received kidneys than died.
Besides the $2 million fine, Kaiser's settlement with California regulators requires the HMO to donate $3 million to a nonprofit group dedicated to helping patients awaiting organ and tissue transplants.