General manager Gerry Toms says security measures will be “a stage higher” than usual.
He was speaking as concerns about the London Games were raised after a swimmer disrupted the Boat Race.
The British Olympic Association said it would do all it could to protect Games athletes.
Cardiff will launch the Olympics when the stadium hosts the first events – two women’s football matches – on Wednesday, 25 July.
The stadium will stage 11 matches in total, including two quarter-finals.
After the Boat Race was delayed on Saturday, British Olympic Association chairman Colin Moynihan said it could take just “one idiot” to cause disruption.
Mr Moynihan said that was why so much security was needed to minimise the possibility, although it could never be removed completely.
Mr Toms told BBC Radio Wales that he had a great deal of sympathy for the organisers of the Boat Race.
“Obviously they plan their contingencies for what they can reasonably expect to happen but there again who would have thought that someone would take such action?” he said.
“The whole purpose of public events… is to allow the people to engage with what’s happening in front of them, to give them the best view, to get them as close to the action as possible.
“And in doing so of course you have to give up certain parts of security you would like.”
Mr Toms said putting on a major event such as the Olympics was about minimising the risks, but they could not be eradicated.
“What you need to do is put in place all reasonable plans. If you take the Millennium Stadium as an example probably we have over 40 different contingency plans that deal with different aspects of what we think could happen.
“The most common for us of course in a sporting event is that someone who wants to get on the pitch.
“But we have a plan in place for that – it’s tried and tested, and if it doesn’t work as well as we expect we go back and revise it. In the Boat Race I’m sure that’s what they’ll do.”
Mr Toms added: “So we’ve got our own contingency plans which are very good.
“But the level of security of the Olympics will be a stage higher and we’ve been working very closely with Locog (the London Organising Committee of the Olympic and Paralympic Games) and we’ve been doing that for 18 months to make sure that we get the right balance about allowing the public the right to enjoy the Games.
“And that’s what it’s all about. And yet have in place the proper measures to deal with things if and when they occur.”
Mr Toms confirmed security would be higher than ever for the Olympics.
“It’s a huge event. It’s similar to holding a government conference such is the state of security, rightly so.
“So there’s a lot of extra work to be done and that plan at the moment is well in place.”