Cross-strait relations have worsened dramatically since Taiwan's president Tsai Ing-wen took power last year and Beijing has cut off all official communication with Taipei.
Taiwan's foreign ministry said Friday it had protested to the UN over the latest incident.
"The UN claims to respect freedom for all, regardless of race, nationality, political or other identities... To serve the political purpose of a particular member nation goes against its mission," it said in a statement.
The ministry confirmed a Taiwanese professor and three students had not been allowed to listen to an open session from a public gallery at the Office of the High Commissioner for Human Rights.
According to Chinese-language website UP Media, staff told labour relations professor Liuhuang Li-chuan of Taiwan's National Chung Cheng University and her students that their passports were invalid documents.
They said "Taiwan is not a country", and the group needed China-issued identification, the report added.
Liuhuang sought help from the director-general of the UN Office at Geneva, Michael Moller, but said Moller told her nothing could be done as "Taiwan isn't following the 'one China' policy".
"Am I speaking to a spokesman for China?" Liuhang wrote on her Facebook page.
A UN Office spokeswoman did not comment directly on the incident, but told AFP that visitors to the premises must present an identification document that is issued by "one country that is recognised as a state by the General Assembly".
The democratic island views itself as a sovereign country, although it has never formally declared independence.
It has been ruled separately since Nationalist forces under Chiang Kai-shek fled there in 1949 after losing a civil war on the mainland.
Chiang still saw himself as leading the "Republic of China" which remains Taiwan's official name.
Taipei held the "China" seat at the UN until 1971, when recognition was switched to Beijing.
The governments in Taipei and Beijing insist countries can only recognise one of them as legitimate and most have sided with China as its global and political clout has grown.
Taiwan participated in some international forums when cross-strait relations improved under former president Ma Ying-jeou.
But since Tsai took the leadership, it has been repeatedly shut out.
Beijing is also pressuring Tsai by wooing Taiwan's dwindling allies.
Taiwan is left with only 20 ally states including the Vatican, with predictions that number will shrink further.