Scottish Justice Secretary Kenny MacAskill has reiterated to parliament that specific funding is being provided to increase police officer numbers.
His comments came after claims that civil servants have been attempting to "call the shots" on police funding.
Grampian Police Chief Constable Colin McKerracher said he was told cash would be withheld if forces missed targets to maintain increased levels of officers.
Mr MacAskill added police chiefs were worried about "UK government" cuts.
The row began after Mr McKerracher told the Herald newspaper that, during a meeting, civil servants were told that police forces would have to cut officer numbers.
On the civil servants' response, Mr McKerracher stated: "They said, 'we just won't give you the funding for the last tranche'.
On Wednesday, Mr MacAskill told the Scottish Parliament that the SNP was delivering on its commitment for 1,000 additional officers, having already met the costs of taking on 801 police.
He said funding to recruit the final 201 officers would be provided "when the additional officers are in place".
"This government is providing the costs of recruitment, training and salaries of the 1,000 extra officers. Extra funding specifically to recruit 1,000 extra officers," said the justice secretary.
"It should not be used for any other purpose."
Mr MacAskill said he laid out the government position with chief constables at the meeting, on 18 January.
The minister accused the last UK government of cutting £500m from Scotland's budget, while a new £6bn reduction programme was on the way, adding: "At that meeting, chief constables also shared their concerns over future budgets.
"They have heard dire warnings coming from UK parties of cuts to come and, like me, they are worried."
Labour justice spokesman Richard Baker asked Mr MacAskill if he recognised police fears about their ability to keep increased numbers of officers.
"This sorry episode shows the Scottish government has been caught red-handed trying to fiddle the figures on police numbers and brought to book by our most senior officers," he said.
Tory justice spokesman Bill Aitken said the meeting showed a "clear level of mistrust between senior members of the police force and the Scottish government".
He asked Mr MacAskill, who insisted he had an "open-door policy" with police chiefs: "Will the cabinet secretary tell us what action he proposes to break down the obvious atmosphere of mistrust that seems to exist between sections of the police force and the Scottish government?"
The Liberal Democrats' Robert Brown said the SNP government was "playing politics" with police funding, adding: "This statement from the cabinet secretary has not answered any of our questions, it has just added more to the pile."
Mr McKerracher previously said of the alleged civil service comments: "It was a threat and a refusal to acknowledge the situation we're in.
"It is symptomatic of their power creep. It is not meant to be civil servants calling the shots."
Mr McKerracher also told the newspaper: "The civil servants are now more and more running policing.
"Five or six years ago they used to be hard task-masters but they would still respect and listen to chief constables. Now they have grasped the policing agenda as their cause celebre."