The man in charge of Ontario’s police watchdog agency issued a strong rebuke Thursday against Toronto police Chief Bill Blair, saying the city's top cop is not doing enough to ensure his officers co-operate with investigators.

Speaking Thursday on CBC Radio’s Metro Morning, Special Investigations Unit director Ian Scott said he’s flagged 106 cases in which he believes Toronto officers fell short of their mandated obligation to co-operate with SIU investigators.

Listen to the interview Click here to listen to Metro Morning host Matt Galloway's full interview with SIU director Ian Scott.

Scott told host Matt Galloway that Blair has provided only one "substantive response" to those letters, in a case about blacked out police notes.

"It tells me that in an attempt to develop a protocol on issues of co-operating with the chief of Toronto police, I’ve had a lot of difficulties," Scott said.

"The easiest thing to do is to look into the issues I’ve raised in the letters and give me a written response, which is all I’ve asked. A lot of these issues frankly can be resolved by the chief looking at the issue and figuring out ‘is this a conduct issue? Is it a training issue?’ I’m not looking for police officers to be internally disciplined over and over again.

"If you have a leader that buys into the concept of public confidence and confidence in oversight like the SIU, then I think it kind of trickles down."

Scott's comments on Metro Morning sparked a response from Mark Pugash, Toronto police spokesperson.

In a statement to CBC News, Pugash said Toronto's police chief has no legal obligation to respond to the SIU director.

"Ian Scott is going way outside his mandate," said Pugash. "The job of the chief is to report to the Police Services Board, that's what the law requires. "Chief Blair's record shows his support for civilian oversight."

The SIU is a civilian agency that investigates when someone has died, suffered serious injury or alleges sexual assault in an incident involving the police.

Scott, whose term as SIU director ends this fall, made his appearance on Metro Morning a week after a Toronto police officer was charged with second-degree murder in the shooting death of Sammy Yatim. The 18-year-old died after he was shot multiple times aboard an empty streetcar in a confrontation with police last month.

Yatim video 'ratcheted up public interest'

While not able to comment about the specifics of the Yatim investigation, Scott said widely circulated videotapes of the shooting have "ratcheted up public interest" in the case.

He added that while a videotape is crucial evidence in SIU cases, it can provide only "part of the matrix" of an investigation, along with statements from officers and witnesses.

Galloway asked Scott about the SIU’s low rate of conviction for officers.

"Prosecutions against police officers … are very, very tough," said Scott. "[Police] are well funded. The police officers come to court with a previously good character and they have an equitable basis that the average person coming into the criminal justice system simply doesn’t have."

Caught between police officers and those calling for accountability for their actions, Scott said the SIU has a difficult mandate.

"At the end of the day my job is to apply the facts to the law," he said. "This isn’t a popularity contest here. I’ve often said there are two lineups of people outside the SIU: discontented police officers and discontented complainants and their families. Because every time you make a call here, someone is going to be unhappy."