Sir Stephen House said the vast majority of such encounters were carried out "properly" but he admitted having "concerns" about allegations of officers recording "ghost searches".
Police Scotland has seen a major rise in the number of stop and searches conducted outside Strathclyde.
The tactic, pioneered by Sir Stephen when he was chief constable of the Glasgow-based force, has been rolled out across Scotland over the last 12 months as a key part of his drive against violent crime.
There have been claims some of 500,000 stop-searches recorded in the last year were faked. Officers do not need to provide names and addresses for the subjects of negative searches that turn up no weapons or drugs.
Sir Stephen said he was not aware of such allegations but added: "I'm not naive enough to think that there aren't occasions where, out of the number of stop and searches we do, there aren't one or two that we feel are not high quality. Unfortunately, on occasion, you get cops that cut corners. The vast majority of them are done properly."
He added that "precious few complaints" were made about stop searches, but when it was put to him that there would be no-one to complain if some searches were made up, he said: "Well, yeah, some of them are being made up. You're not suggesting the majority are."
Graeme Pearson, the Scottish Labour spokesman for justice and a former police chief, said: "There's a growing acknowledgement that for negative stop- searches nobody at headquarters can check to see if they have taken place."