It also denied a visa to a senior representative of Amnesty International.
The moves underline Vietnam’s growing confidence in its crackdown on government critics and its rejection of foreign criticism of its record.
The Secretary-General of the International Federation of Human Rights (FIDH), Debbie Stothard, was detained at the airport in Hanoi and held overnight before being deported to Malaysia.
She said on Facebook that she had been blacklisted under Article 21 of the immigration law, which blocks entry to anyone seen as a threat to national defence and security.
The WEF said it regretted the move and that it would continue to try to facilitate her participation.
FIDH is an umbrella group that represents some 180 human rights organisations in a hundred countries.
Vietnam is increasingly willing to show its anger at what it sees as foreign interference in its internal politics.
For some years it had indicated that it was open to human rights dialogue and maintained it was attempting to improve its record.
However, the consolidation of hardliners around the Communist party boss, Nguyen Phu Trong, in 2016, ushered in a much harsher climate.
Analysts say that the leadership has been further encouraged by the Trump administration’s lack of interest in promoting human rights.
Ms Stothard said the inconvenience she faced was nothing compared to the attacks sustained by Vietnamese human rights defenders.
Amnesty International’s director of global operations, Minar Pimple, was also denied a visa to attend the forum.
Amnesty condemned the decision as an attempt to stifle debate.
The organisation has produced regular reports cataloguing human rights abuses in Vietnam.