Mark Saunders told the CBC radio show Metro Morning he does not support racial profiling or routinely stopping innocent people, but stopped short of denouncing the practice known as carding.
He told the show that "when it's done right, it is lawful."
Critics of the practice have said it tends to disproportionately affect young black men and has led to distrust of police.
Mayor John Tory joined their ranks this weekend, telling a news conference he intends to go before Toronto's police board on June 18 and call for the elimination of carding.
The practice was suspended in January by then-police chief Bill Blair, but Saunders has defended it as a valuable tool.
The issue could also be headed for the courts after a Toronto man launched a constitutional challenge against the controversial practice on Wednesday.
George "Knia" Singh, who describes himself as a Toronto-born African-Canadian, alleges the information-gathering scheme amounts to racial profiling that puts people in danger.
Singh, through his lawyer, has filed a notice of application for judicial review of the practice, arguing the Toronto police services board and the police chief have violated his charter rights.
Saunders told Metro Morning that police stops are "intelligence-based" and meant to help investigate "the criminal element in the community."