He said people's rights could not be deprived "by any country, government, political party or individual".
Chen maintained, in a meeting with Scott Horton, President of International League for Human Rights, that on 20 March, the day of the Taiwanese presidential election, he would ask China to remove its missiles targeting the island and renounce the use of force against Taiwan.
The president stressed that the deployment of 496 ballistic missiles along China's southeastern coast posed a great threat to the people of Taiwan.
"To advance Taiwan's democracy and safeguard peace, security and stability in the Asia-Pacific region, (we) will ask China on the March 20 presidential election day to immediately remove missile deployment and openly renounce the use of force against Taiwan," he said.
'Basic human right'
Chen's plans to hold the "anti-missile, anti-war" referendum provoked a stinging rebuke from the United States and anger from China, which considers the island part of its territory awaiting reunification, by force if necessary.
Washington and Beijing fear the referendum would eventually lead to a vote on Taiwan's independence from China.
"The 23 million people in Taiwan should enjoy the basic human right of holding referendums like people in the rest of the world. This right cannot be deprived by any country, government, political party or individual," Chen told Horton.
"The comments and actions made by the leader of Taiwan indicate that he may be willing to make decisions unilaterally to change the status quo, which we oppose"
The Taiwan leader also referred to the "American spirit" in expressing his disappointment at US President George Bush's rebuke of his referendum proposal.
"The American spirit should not take the missile deployment as a matter of course, nor should it regard the pursuit for peace and democracy by the Taiwanese people as provocation," Chen said.
Bush on Tuesday voiced Washington's strong disapproval of the proposed ballot.
"We oppose any unilateral decision by either China or Taiwan to change the status quo," Bush said after talks with Chinese Premier Wen Jiabao.
"And the comments and actions made by the leader of Taiwan indicate that he may be willing to make decisions unilaterally to change the status quo, which we oppose," Bush added.
Chen said, "We want to maintain a status quo of peace and stability instead of one of missile deployment and military threat."
Washington has observed the "one-China" policy since it switched diplomatic recognition from Taipei to Beijing in 1979.
Bush (R) stands with Chinese Premier Wen Jiabao against Taiwan independence
Wen said China would not tolerate any moves towards independence by Taiwan.
"The attempts of Taiwan authorities, headed by (President) Chen Shui-bian, are only using democracy as an excuse and (an) attempt to resort to a defensive referendum to split Taiwan away from China," Wen said.
US opposition weighs in
Congressional Democrats slammed Bush for abandoning Taiwan in its push for democracy, exposing as hollow his oft-stated commitment to promoting "freedom" around the world.
"By rebuking (Chen) for advocating the most basic of democratic values - the right of free people to express their views by voting - President Bush badly damaged the tradition of the United States of standing with those who want democracy and freedom," said House of Representatives Democratic leader Nancy Pelosi.
Chen said the 2004 presidential elections, in which he is running against Lien Chan from the Kuomintang (KMT), would be a contest between "one side, one country" and "one China" ideologies.
The KMT favours co-existence with the mainland and an eventual reunification of the two rivals, separated in 1949 at the end of a civil war.