Mr Clinton will include the security funding in the budget request he is scheduled to sumbmit to Congress next month.
About $90m of the total cost of the programme will be spent on developing new technologies to thwart cyber-terrorists.
The president said people using computers had the power to take humanity to great heights by increased knowledge - but they could also create havoc, paralysing businesses and governments.
"There has never been a time like this, in which we have the power to create knowledge and the power to create havoc, and both those powers rest in the same hands," Mr Clinton said.
He said the feared threat to computer networks from the Y2K computer bug - a problem caused by the millennium date change - highlighted just how much the country was dependent on computers and their increasing inter-connection.
Outlining the programme, Mr Clinton said the aim was to protect national security and the rights of American citizens.
"It is essential that we do not undermine liberty in the name of liberty," he said.
Cyber warfare
The programme is the result of a study ordered by Mr Clinton into ways to protect America's computer systems from attacks by cyber-terrorists, which could cripple key sectors of the economy.
The head of counter terrorism efforts for the US National Security Council, Richard Clarke, said on Friday that nations that had developed cyber-warfare capabilities also posed a threat to the US.
"We are aware now, over the course of the past two years, that several other nations have developed offensive information-warfare units, organisations, tactics, doctrine and capability," Mr Clarke said.
"That doesn't mean they're going to use then, but it means that they are developing them, they're getting better all the time."
Mr Clarke did not specify which nations he was referring to.
Clinton's concern
Mr Clinton has often expressed concern about the emerging threat that other governments, hackers and thieves pose to a world that relies heavily on new technology.
His concerns have focused on the threat of computer hackers breaking into sensitive government and business computer networks, stealing and destroying information, raiding bank accounts, running up credit card charges and extorting money by threats to unleash computer viruses.
Computer viruses, such as "Melissa", which was released early last year, have highlighted the government's vulnerability, according to the GAO.