Moreover, previously undisclosed draft audits prepared in 2005, near the end of his first term, show that Mr. Thompson’s handling of the city’s pension funds had been so worrisome that state regulators suggested his office be stripped of responsibility for investing them, a finding that casts his managerial record in an unflattering new light.

In an interview, Mr. Thompson emphasized that he was not the only one with influence over investment decisions and that political support played no role in the process. While the comptroller’s office makes recommendations for which investment managers to hire, the selections are reviewed by outside consultants and boards of trustees for the pension funds, though former and current officials say the comptroller’s recommendations are almost always followed.

“No one received any favor based on a contribution,” Mr. Thompson said in an interview. “Everything was done on the merits.” The 2005 draft audits, he said, were a politically motivated attack aimed at his predecessor, whose term covered more than half of the period the auditors examined. “That had little to do with me,” he said.

After Mr. Thompson was elected in 2001, he vowed to overhaul the Bureau of Asset Management, the key arm of the comptroller’s office that invests the holdings of the five city pension funds, which now total more than $100 billion. The bureau then was in dire need of modernizing. But records show his efforts were slow and delivered mixed results.

He created a new position for a chief investment officer. But he had difficulty recruiting and keeping anyone in the job. One appointee left after several weeks; another lasted 13 months.

He also spent more than $400,000 on consultants to diagnose the bureau’s problems and recommend solutions. Their report, delivered in August 2003, suggested the place was being run almost by instinct and guesswork: the investment unit still lacked an overall strategy, standard operating procedures and a risk-management strategy. The lack of clear governance policies, the report said, compounded the structural challenges of having five separate boards of trustees, each with representatives from different agencies and unions.