House said the vast majority are conducted "properly" but he admitted having "concerns" about allegations of officers putting in ghost entries into the system.
He also defended his right to a controversial allowance to help pay his housing costs, saying: "I took the package as offered to me, and I'm not about to renegotiate it."
Stop and search is a tactic promoted by House and used to catch suspects in possession of drugs, knives and stolen goods.
Over 500,000 searches have been carried out since the formation of Police Scotland last year.
However, former officers told this newspaper that police were making up bogus stop searches due to the pressure from their bosses to keep the numbers up.
The system for entering details of a search does not require a name and address to be input, an omission it is claimed results in bogus entries.
In an interview with the Sunday Herald, House said he had not heard this, 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."
Asked if the allegations concerned him, he said: "Of course it concerns me." 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."
On his housing allowance, the perk older officers still receive, he said: "I have to say to you, it's been part of my terms and conditions since 1981 ... It's the same for every single officer who joined before 1994."
On whether it was unfair for him to get help with his mortgage while civilian police staff jobs were being cut, he said: "You call it that, 'special help with your mortgage', but it's just another line in the pay packet. I don't see it like that ... [Police staff] took the job that they took under terms and conditions. They have taken voluntary redundancy under very clear terms and conditions. Each person deals with life in their own way."
Gerry Crawley, a regional organiser for the trade union Unison, said: "We are all meant to be in this together, but the cuts are focused on support staff. Not all police officers get a cut of the £10 million housing allowance, only a proportion. I'm sure most officers would support the retention of jobs across the country, rather than see some colleagues get an historic allowance. It is not right and not fair."
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.
"When I asked about this issue at the sub- committee on policing, it was acknowledged there was a problem."