Sean Dyche criticised the time it took for stewards to tackle a Blackburn fan who confronted Burnley players and revealed he almost came onto the pitch himself.
The unsavoury incident happened after Jack Cork had headed Burnley into the lead in the 27th minute of their 2-0 Carabao Cup second-round victory at Ewood Park.
Two home supporters ran onto the pitch, with one heading straight for a group of Burnley players as they made their way back to the centre circle.
Pictures emerged of the fan with his hand to Ashley Westwood's throat before he was tackled to the ground by the Clarets midfielder.
Both supporters were arrested along with a Burnley fan who was escorted out of the stadium after setting off a flare, also after Cork's goal.
There was a huge police presence for the clash between the bitter rivals, and Burnley's following of more than 5,000 was escorted by police along the M65 in buses.
Clarets boss Dyche said: " There used to be a time when if people got on a football pitch it was kind of in jest, it could almost be laughed at.
"Now there's all kinds of things going on in the world, and when people get on a football pitch it has to be stopped very quickly. That's not just this football club, that's across the board. Stewards do a terrific job but they've got to get on quick.
"It seemed a long time before anyone did anything and then our players had to eventually defend themselves, and that can't be right anywhere in football.
"We were going to go on because I can't have that. Not to do anything ridiculous just to say 'this can't happen'.
"To think you go to the extreme (of escorting fans) and then someone just wanders onto a football pitch is a bit bizarre at least. The safety of players is paramount."
Blackburn manager Tony Mowbray did not see the incident but criticised the actions of the fan.
He said: "It doesn't do anything for our football club and I'm pretty sure the authorities will deal with the people who were involved.
"I'm sure the vast majority if not all the rest of the supporters will be disappointed with the supporter who came on the pitch. It's not what we want to see, it's not what this club's about."
It was the most uncomfortable moment of the night for Burnley, who were in control by the time Cork scored and had several chances to extend their lead before Robbie Brady made it two in first-half injury time.
Dyche, who made eight changes from the Premier League defeat by West Brom and gave a debut to record signing Chris Wood off the bench, said: " I'm very pleased.
"I said before the game I think we've added another layer to the group. We need it and we've still got to further it where we can, and I'm not being too bold, but I think we're in good shape and I think we showed that tonight."
It was another reality check for Rovers, with the two division gulf to their derby rivals painfully apparent.
"I think you could feel the Premier League quality of the opposition tonight," said Mowbray. "I know it's hard to take for Rovers fans to see Burnley that far in front of us at the moment."