Kenny MacAskill said he did not recognise a world where detection rates "are being manipulated", insisting police "do appropriately record incidents".
Addressing questions on stop and search in the Sunday Herald, Police Scotland Chief Constable Sir Stephen 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 Stephen added. His comments were corroborated by Scottish Police Federation general secretary Calum Steele, who said officers "are making numbers up", Labour MSP Graeme Pearson told MSPs.
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 of the police. This is an operational matter."
Mr Pearson said: "The chief constable's admission is corroborated by Calum Steele 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 added: "I think the chief's words have been taken out of context."
Police Scotland figures show that some 519,213 stop and searches were conducted between April and December 2013.