Tania Corbett from Open Doors has said Christians make up a minority in the southeast Asian country, which is mainly Buddhist, and can be singled out.
She said: "It's very hard to be a Christian in Vietnam, currently it ranks at number 20 on our World Watch List [of Christian [persecution].
"You are seen as an enemy of the state, it's a Communist country, where they often see Christians as spies for the West.
"It'll highlight that there are restrictions on religious freedom in Vietnam and that by raising awareness of that and by highlighting that issue more pressure will be brought to bear on the authorities there to allow people greater freedom."
During his visit President Obama called on the Vietnamese government to allow greater freedoms for its citizens, saying that better human rights would improve the economy as well as stability and regional power.
He told the country that freedom of expression is where new ideas happen: "That's how a Facebook starts.
"That's how some of our greatest companies began."
Mr Obama also met with activists and entrepreneurs as part of a push for closer ties with the fast-growing country.
The visit included the lifting of a half-century-old arms sale embargo.
Tania Corbett said believers can pray: "Pray for all of these who're experiencing pressure in a village situation where the majority of people aren't Christian and they find themselves in an oppressed minority."
Listen to Premier's Hannah Tooley speak to Tania Corebett here:
