The force, which deployed officers on 109,000 occasions during the sporting event in Glasgow, is under serious pressure to ensure services are maintained across the country, as officers take time off in lieu, rest days and delayed leave.
It insists it can manage the absences, which it describes as "abstractions", but has officially listed staffing concerns on its risk register in bright red at a maximum 25 points out of 25.
Police Scotland head of human resources John Gillies wrote: "There is a risk that abstractions needed to allow officers to take time accrued during the Commonwealth Games are not effectively and efficiently managed."
The risk register is reported to the force's watchdog, the Scottish Police Authority, and will be discussed by members of its HR committee today.
The single force has raised the risk of staff and office morale falling to "high". Mr Gillies said the force had processes in place to deal with time off in lieu (Toil), but added: "Until the impact of the Commonwealth Games deployment can be assessed it is not known whether these will still be sufficient."
A Police Scotland spokesman stressed the register was simply a tool for gauging the potential scale of problems.
He added: "Plans have been put in place with the support of the Police Federation to allow officers extended time to take any outstanding rest days."
The Scottish Police Federation's general secretary, Calum Steele, stressed that Toil was a problem for the force even before the Games.
He said: "The historic failure of the old forces to address Toil debt was always a risk to the service.
"Failures of the past, however, do not absolve the new service of responsibility."
Scottish Liberal Democrat justice spokeswoman Alison McInnes MSP has questioned whether the national force made enough use of officers from other parts of the UK during the Games.