Kenny MacAskill said he does not recognise a world where detection rates "are being manipulated", insisting police "do appropriately record incidents".
Addressing questions on stop and search at the weekend, Police Scotland Chief Constable Sir Steve House said: "Well, yeah, some of them are being made up. You're not suggesting the majority are. Of course it concerns me."
Any officer caught reporting misleading figures will "get sacked", Sir Steve added.
His comments were corroborated by Scottish Police Federation general secretary Calum Steel, who said officers "are making numbers up", Labour MSP Graeme Pearson told MSPs yesterday.
Mr MacAskill said: "It is regrettable if there are occasions when police officers are not carrying out stop and searches to the usual high standards.
"This is an operational matter for the police, but I will support the chief constable in the actions he is taking."
Mr Pearson said: "The chief constable's admission is corroborated by Calum Steel from the Scottish Police Federation who said: 'Because we have this bizarre approach in terms of stopping and searching, we have police officers that are making numbers up'."
Mr MacAskill said: "I think the chief's words have been taken out of context."
Some 519,213 stop and searches were conducted between April and December 2013, according to Police Scotland. Searches to detect firearms yielded a positive result in 37% of cases, with 166 "firearms or associated items" recovered. Almost 37% of alcohol-related searches were positive and 61,541 recoveries were made.