Two staff bodies for officers will meet Police Scotland chief constable Sir Stephen House soon to discuss allegations that "ghost entries" are being recorded in a bid to inflate the figures.
The high number of so-called consensual stop-searches, some conducted on children as young as seven, is also expected to be raised.
Willie Rennie, the Scottish Liberal Democrat leader, said he was pleased the talks would be taking place.
Stop and search is a policy aimed at catching criminals possessing drugs, weapons and other illicit items.
The searches can either be statutory - where police must have reasonable grounds of suspicion for stopping someone - or consensual, which can only be carried out if an individual agrees.
In the first nine months of Police Scotland, 537,434 stop-searches were recorded, a figure that triggered alarm at Holyrood.
However, allegations emerged that police officers, under pressure to keep the numbers up, had been entering bogus searches into the system.
The computerised recording form does not require the name and address of the person searched to be input, a loophole that police sources said had resulted in the ghost entries.
Scottish Police Federation (SPF) general secretary Calum Steele said recently: "Because we have this bizarre approach in terms of stopping and searching, we have police officers that are making numbers up."
The issue will come to a head when the SPF and the Association of Scottish Police Superintendents (ASPS) meet Mr House to raise concerns. David O'Connor, the president of ASPS, said he supported stop and search, but there needed to be a careful look at whether the alleged behaviour was linked to target-setting. He said: "Talk of ghost entries is something that is doing the rounds. It is quite clear that the figures as they stand need to scrutinised.
"The Chief Constable has sent a couple of very strong messages out that anybody who is involved in that type of behaviour runs the risk of some form of reprimand."
He said the round-table discussion, expected to take place this month, had been requested by the police organisations.
Brian Docherty, the SPF chairman, said he backed "responsible stop and search", but added: "Everyone is agreed that there are issues in stop and search that have to be addressed. Everyone agrees there is a problem with the way searches are being recorded. We need to sit down and sort this out. It's about time we drew a line in the sand and moved forward."
The Scottish Police Authority, which oversees the single force, is conducting a review of stop and search. Justice Secretary Kenny MacAskill has defended the policy, as a vital crime-fighting tool.
Mr Rennie, who has called for an end to consensual searches, said: "Kenny MacAskill's refusal to listen to reason on stop and search has left him looking increasingly isolated. Now it seems that even those charged with implementing stop and search have concerns over how this tactic is being used.
"I am pleased that police representatives are meeting with the Chief Constable to explore the matter. It would be helpful if they could broaden their discussions to include the many people who are concerned."
A Police Scotland spokesman said: "The Chief Constable meets with representatives from ASPS and SPF on a regular basis and discussions will take place on issues they wish to raise."