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 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 Steel, who said officers "are making numbers up", Labour MSP Graeme Pearson told MSPs today.
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 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 figures.
Searches undertaken 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.
Liberal Democrat justice spokeswoman Alison McInnes said: "The Justice Secretary has regularly, and done it again today, defended stop and search by citing offensive weapons, but we know little of what constitutes positive searches and there is a real risk that the detection rates are being manipulated."
Mr MacAskill said: "I don't recognise the world that Ms McInnes paints.
"It seems to me that the clear outcome of a positive search is where a firearm is discovered, which is 37%.
"Alcohol was taken off youngsters, 37%, and indeed the significant progress and success that they have had in making Scotland a safer place from the issues that have blighted so much of our country in the carrying of offensive weapons."
He added: "Scotland is a safer place and equally they do appropriately record incidents so that they are there to be checked as either successful or unsuccessful.
"I think the proof of the pudding is in the eating, and that two things that are clear are that the number of complaints about stop and search are 0.01%, a small number indeed, and equally Scotland is a safer place."