Flower's side completed a handsome 196-run victory over India at a sold-out Lord's yesterday, but things could have been very different had Sachin Tendulkar or Suresh Raina held on for the draw after being reprieved by Billy Bowden.
The New Zealand umpire turned down plumb lbw appeals against both batsmen off the bowling of Stuart Broad on an enthralling final day of the first Test.
As it was, James Anderson was on irresistible form and accounted for both men long before the close, but Flower believes the incidents drew attention to the lack of DRS on lbw decisions in this series.
India have registered their dissatisfaction with the predictive element of ball-tracking systems such as Hawk-Eye and refused to agree to use the technology against England, leaving leg before decisions with the on-field umpires.
Flower now predicts the issue could cause controversy in the remaining three matches of a series, which continues at Trent Bridge on Friday and has already captured the imagination of the cricketing public.
Asked if he was worried there could be trouble ahead, he said: "Yes, I am actually. We almost saw it happen in this Test match.
"It would have been wrong if the outcome of the game had been seriously affected by a couple of those decisions and it was quite right that, luckily, we did continue to create chances. It's unsatisfactory the way it is, there is no doubt about that."
ICC chief executive Haroon Lorgat has pledged to commission independent research into ball-tracking in a bid to persuade any doubters, but Flower reckons they should have acted more decisively on the issue ahead of this high-profile contest.
Flower said, "I don't think there's anything we can do, but I think the ICC should be stronger in taking a lead on these issues".
"They are the world governing body and they should lead. I don't think it's unfair to say they haven't led on this topic.
"We all know that it is not going to be 100% accurate, but we also know you get more right decisions using it, so let's not quibble about millimetres here when we know you get more right than wrong. That's why most Test-playing nations want to use it.