Reacting to the UN decision, David Wang, a spokesman for Taiwan's foreign ministry, condemned what he called the "political reasons" for rejecting the bid.
"The 1971 resolution should be reviewed, as it fails to address the question of the right of representation and participation by the people of Taiwan," he said.
Last week Chen Shui-bian, the president of Taiwan, submitted a formal application for Taiwan to rejoin the UN under its own name.
Taiwan has previously made 14 applications to rejoin the UN, all under the "Republic of China" name.
Name-dropping
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Taiwan split from mainland China at the end of the Chinese civil war in 1949
Beijing regards Taiwan as part of its territory, and says it will use force if it ever declares independence
Beijing and Taipei both say they are the legitimate government of all China
Taiwan has been a multi-party democracy since 1996
Taiwan's defence ministry says China now has nearly 1,000 missiles aimed at the island
The US is the major arms supplier to Taiwan and has warned China that any attack on the island would be viewed with "grave concern"
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Taiwan
continues to be formally known as the Republic of China, although recently Chen has increased the use of the name Taiwan as a way of solidifying the island's separate political status.
Earlier this year China hit out at Chen's efforts to drop the name "China" or "Chinese" from several state-owned Taiwan firms.
The move was also criticised by several opposition figures in Taiwan itself where relations with the mainland are a hotly debated issue.
Chen has announced plans to hold a referendum on Taiwan's UN membership later this year to back up his bid to join the organisation.
On Tuesday David Lee, Chen's presidential spokesman, said the UN's latest rejection would not derail those plans.
"Entering the UN is the mainstream opinion in Taiwan," Lee said. "The referendum will enable us to have our voice heard in the world."
Taiwan split from mainland China at the end of the civil war in 1949, although Beijing continues to claim the island as part of its territory.
Beijing has firmly opposed Taiwan's bid to join the UN, saying it is a step toward formalising the island's de facto independence.
In 2005 the mainland government passed a law threatening the use of force if Taiwan ever declared it was formally breaking off from the mainland.