A Catholic bishop is opposing Austrian government plans to build a border fence to deny entry to refugees by refusing to cooperate with authorities and arguing that it is against the Pope's wishes and not the answer to Europe's refugee crisis.

"A fence would contradict the spirit of the Gospel, Pope Francis's clear message to Europe, and in particular for a diocese that was in the shadow of the Iron Curtain for decades," Bishop Aegidius Zsifkokvics of Eisenstadt told the AFP news agency.

''We need to tackle today's problems at their root and that means: stopping organised human trafficking, stopping sales of European arms, stopping war and the deliberate destabilisation of the Middle East," he said, according to the Daily Mail.

The proposed nine-kilometre fence on the Hungarian border near Moschendorf would cross two properties owned by the Church.

The fence was reportedly ordered by the government of Catholic Chancellor Werner Feymann in a bid to cut the number of migrants looking to avoid controls at authorised crossings.

But the 53-year-old bishop contended that building the border will not change everything and that the refugee problem will worsen unless it is addressed from the roots.

Zsifkokvics likewise stressed that the Church had always opened its doors throughout the refugee crisis, and that "now is not the time to change."

During the worst refugee crisis last year when 200,000 people crossed the border at (nearby) Nickelsdorf in six weeks, the bishop said they "provided around a thousand emergency places in church buildings for exhausted families, for women, children and old and weak people."

''And now we are supposed to build a fence on Church lands?''

According to reports, Austria took in 90,000 refugees in 2016 and saw almost 10 times that cross through its borders as they searched for asylum in Germany and throughout Scandinavia.

The stance of the Catholic Church in Austria comes as migration debates heats up the nation and the refugee crisis worsens as conflict in the Middle East rages.

Last year, the country served as a transit country for hundreds of thousands of migrants and refugees seeking to reach countries in northern Europe, such as Germany and Sweden, and has also seen an increase in the number of asylum claims in the country, reports say.

More than 1 million people arrived in Europe last year, but their arrival was reportedly met with the rare closure of borders and plans to build fences, effectively shutting down the Balkan route to other countries.

Amid a new influx of refugees this year, countries are planning to erect several barriers, including at Moschendorf and at the Brenner Pass on the Italian border, says the Mail.