Fr Nguyen Dinh Thuc, believes he was prevented from travelling as a punishment for his activism on behalf of fishermen who lost their livelihood after the Formosa Company steel plant disaster in 2016.
A notice signed by the immigration authorities states that Fr Thuc was prevented from travelling for reasons of "national security and social order".
Christian Solidarity Worlwide's (CSW) chief executive Mervyn Thomas has condemned Vietnamese authorities for their actions.
"The suggestion that this has been done for reasons of national security is completely unfounded and is a clear reprisal for peaceful advocacy," he said.
"We call on Vietnam to allow the priest to travel freely, and to cease all harassment."
CSW said it continues to receive reports of severe violations of freedom of religion or belief against every major religious community in Vietnam, including Catholics. The charity said individuals in remote areas who are both ethnic and religious minorities, such as the Montagnard ethnic minority Catholics and Protestants in the Central Highlands of Vietnam, suffer the most severe abuses, including disruption of religious services, beatings, threats and intimidation and damage to properties used for religious services.
CSW added Catholics who defend the rights of others are subject to arbitrary detention, sometimes leading to lengthy sentences.
Nguyen Van Hoa, a young Catholic activist who also helped victims of the Formosa environmental disaster, was sentenced to seven years in prison in a closed trial in November 2017.
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