Reports emerged after England's 5-0 Ashes whitewash defeat to Australia that Flower gave the ECB an ultimatum.
It had been suggested that Flower warned that he would step down from his role if Pietersen remained in the England team, but Flower rejected those reports.
"We went through tough times and people want to make up stories," BBC Sport quotes Saker as saying. "Kevin has been the same as he has always been. I'm sure what's being reported is nowhere near the truth.
"The relationship between Kevin Pietersen and Andy Flower hasn't changed from where I'm sitting. That's what happens. When you are losing these things come out quite often."