The ICC security arrangements were already thorough, but a more visible constabulary presence has been promised at venues, hotels and transport facilities.
Armed soldiers have also been deployed across the country to assist police.
Few details have been revealed because of concerns it will dilute the overall objective for vigilance.
"Come in the knowledge that we will make this a safe and secure tournament," Flanagan said at a media conference in London.
"Don't let the terrorists have their way. In my experience, sport can be a wonderfully positive influence in the face of adversity and terrorism. We have seen that in South Africa. I saw it first hand in Ireland [during the Troubles].
"I have every confidence we will not yield in any way to terrorists' intentions. I would ask the public to be vigilant and apply the old adage: if they see something, say something. But come to our matches."
Getting into the grounds might become more complicated for fans. Searches of bodies, bags and vehicles will be intensified, although express lanes for light travellers could offer respite.
The New Zealand team have suffered few restrictions to their daily routines. However, South Africa, who lost to England by 72 runs in the first of their three-match one-day international series at Headingley on Wednesday, were more concerned.
"There was a lot of chatter at the breakfast table," South African team manager Dr Mohammed Moosajee said before the opening match.
"I'm sure you will understand we have genuine concerns. The players are uneasy.
"We've had constant communications with the ECB and guarantees have been put in place that security arrangements will be supplemented [by respected adviser Reg Dickason].
"Make no mistake, if this were any other country, people would be asking whether this series and the Champions Trophy were at risk."
