The problem lies in the way officers classify searches. Where an officer is conducting a search for weapons such as knives, but finds drugs instead, the results are recorded as a positive search for weapons.
As a result, the recording system has given the impression of 1506 more weapons finds than there actually were in the force's first year.
MSPs yesterday hit out at the "misleading" and "dodgy" figures.
Stop and search is a tool strongly associated with Police Scotland Chief Constable Stephen House, who rolled it out to the single force after using it extensively at the old Strathclyde force, which he headed.
But the Sunday Herald has exposed a number of flaws with the policy, including officers entering "ghost" searches into the police computer to keep the figures high.
This newspaper also revealed Police Scotland had "consensually" frisked children, babies and toddlers, a practice that was banned last week.
More evidence that the stop and search policy is in disarray can now be revealed. House and Justice Secretary Kenny MacAskill have both said searches are a key plank of the strategy to combat knife crime.
The chief constable said stop and search was "one of a range of policing tactics we want to use to deter people from carrying knives in the first place".
Similarly, the Cabinet minister told Holyrood in April that thousands of weapons searches yielded a "positive result".
However, Police Scotland's end-of-year crime report raises questions about the picture being presented to the public.
It noted that the total number of detections of offensive and bladed weapons - 3,712 for the first 12 months - was 1,506 lower than the number of "positive searches" for the same category. According to the report, the discrepancy exists because a positive search for "offensive weapons" does not necessarily mean a weapon has been found.
Recording procedures mean the find could be illegal "items".
A spokesman for Police Scotland confirmed that a knife search which, for example, only found drugs, would be recorded as a weapons search that yielded a positive result.
This is due to the police system recording the reason for the search, and whether it was successful, rather than the item discovered.
The gap between the 3,712 weapons detection figure and the "positive" stop search number is 41%.
Put another way, 29% of the 5,218 positive searches for offensive weapons in the first year of Police Scotland did not find weapons. Thousands of successful searches in other categories, such as drugs, may have found something else.
Kath Murray, an Edinburgh University academic and stop and search expert, said: "It's difficult to have a mature and transparent debate on such an important issue when Police Scotland have overstated the number of weapon detections by 40%. These inconsistencies highlight that this policy has not been properly regulated, nor made accountable, and add to the growing concerns about the way in which this contentious policy has been justified."
Scottish Liberal Democrat justice spokesperson Alison McInnes MSP said: "The more Police Scotland's approach to stop and search is put under the microscope the more worrying it all becomes."
Graeme Pearson, Scottish Labour's justice spokesman and former top police officer, said: "The figures published have at best been misleading and provide little in the way of understanding what works."
Police Scotland Assistant Chief Constable Wayne Mawson said: "A positive stop search is one which is either conducted with the consent of a person being searched or is done in execution of some explicit lawful power, and in consequence of which some item is recovered where possession of same infers criminality on the part of the person being searched or some other person; or compromises the safety of that person or some other person."