Sir Stephen House said any officer caught falsifying figures will be sacked, but he conceded that it does happen.
He said: “Well, yeah, some of them are being made up. You’re not suggesting the majority are. Of course it concerns me.”
Mr House was speaking out after unnamed officers claimed that “500,000 or so recorded stop searches were misleading”.
The rollout of stop and search has been one of the most controversial aspects of Police Scotland, particularly in rural areas where communities have complained about the introduction of “Glasgow-style” policing.
Holyrood’s sub-committee on policing has urged Police Scotland to listen to “whistleblowers” raising concerns about a target culture at Police Scotland.
But officers will not speak out “because it is not good for their careers”, convener Christine Grahame told MSPs in November.
Seizures of drugs, weapons and alcohol increased by a third in the first eight months after the single force was introduced last April despite a slight fall in the number of people being searched, according to official Police Scotland figures.
Police searched 519,213 people and came up with a “positive result” in nearly a fifth of cases.
Before the merger, Scotland’s eight forces searched almost the same number of people in the last eight months of 2012 but only found something in about one in seven cases.
Scots may now be six times more likely to be stopped than people south of the Border, recent Edinburgh University research suggested