A Christian Church in southern Hungary is thanking God and the Hungarian government for protecting its people by sealing the country's border with Serbia to stem the influx of Muslim migrants who want to seek refuge in their area.

"We are thankful to God that our country has a government now which regards the protection of our country and people as a task given by God ... while it promotes and practices brotherly love toward those arriving in our homeland," the Reformed Church of Csongrad diocese said in a statement picked up by Reuters.

The church said the border protection action taken by the Hungarian police was "professional, proportionate and humane."

"We are aware that most migrants arrive from countries which are open enemies of Jesus Christ and Christianity and in which Christians are persecuted for their faith. Those who come here may not have participated in this actively, but it is enough if they agreed with the persecution or did not raise their voice against it, while coming here they demand their human rights to be observed," the church statement said.

Hungary, a landlocked country whose government has been criticised by its European Union neighbours for its anti-foreigner stance, has reportedly become a main transit route for hundreds of thousands of migrants arriving via the Balkans to the south.

Reuters said more than 280,000 migrants fleeing conflict and poverty in the Middle East, Asia and Africa have passed through Hungary in central Europe this year seeking sanctuary in the wealthier countries of the western EU. Csongrad county lies on the border with Serbia.

Andras Juhasz, dean of the Protestant diocese, told Reuters that the church was compelled to raise its voice given "what was happening in this part of the country.''

"We felt that Christian people could not remain silent in this situation," he said.

Hungarian Prime Minister Viktor Orban said his government has also toughened its anti-migration measures, vowing not to let mainly Muslim migrants threaten Hungary's Christian traditions.

In the same statement, the church said any criticism of Hungary for protecting its borders was "unfounded and unacceptable."

The church added that it was providing help for migrants in the name of brotherly love, praising the work of the Hungarian Reformed charity and refugee mission.