The Scottish Police Federation said it had been contacted by "disgruntled" members unhappy about shift patterns during Glasgow 2014.
The federation stressed the numbers were "fairly small" given the size and scale of the event.
Chairman Brian Docherty said: "I can confirm we have received complaints from officers about the way their shifts have been changed at the last minute or the length of shift they're having to do or the travelling they're having to do to get to and from events.
"Every issue we get sent to us we are doing our best to get addressed with the service and the Commonwealth Games planning team as a matter of priority.
"Some can be fixed very quickly, i.e. bottled water or refreshment breaks, and nine times out of 10 they are.
"There have been a couple of issues which we have raised with the Chief Constable and through his force executive he has been actively trying to get these matters addressed.
"With the size of the event unfortunately, being the first thing we've ever had like this in Scotland, I think it's proving to be very problematic and I'm sure there's going to be a number of learning outcomes on the other side of this."
Mr Docherty said officers were doing a "terrific job under very testing conditions".
He said: "People are going to be probably stretched to the limit a wee bit on what they can do as far as resource is concerned.
"There are circumstances at times that can't be helped.
"Being police officers we accept at times that there has to be some long shift work.
"We will be in a position at the end of the Games to know exactly how many people are disgruntled and have been badly affected by it, but at the moment the number of complaints we're getting - bearing in mind the number of officers involved - seem to be fairly small."
Responding to reports that police officers had allegedly soiled themselves during long shifts, Mr Docherty said the federation had been unable to identify anyone involved, despite its best efforts.
A Police Scotland spokeswoman said: "A detailed resource plan has been developed to make sure that there are sufficient police officers policing the Games as well as making sure that sufficient police resources remain in our communities to continue to keep people safe.
"The welfare of officers is a matter of importance to the command team leading the operation and to Police Scotland.
"Anyone who has any concerns is reminded again to speak to their supervisor or Federation representative."