Thousands of Christian and Muslim pupils in Israel missed the start of the academic year today as the crisis over Christian education deepened with a shutdown that forced children and teachers to stay at home.

The 33,000 pupils, their parents and teachers claim they are discriminated against in Israel's education budget and are calling for the the same treatment as other schools. The stoppage affects all Israel's 45 Christian schools and their 3,000 teachers.

Parents pay about a third of the cost of educating their children at the schools, which are among the highest achieving academic schools in Israel. Two years ago, the government cut the subsidy it gave Christian schools from between 45 and 65 per cent to about a third or less of the schools' budgets.

About four in ten of the pupils at the Christian schools are Muslim, and the rest are Christian. Most of the schools are of Catholic foundation.

Israel's education minister Naftali Bennett who has met church leaders in Israel has given them reassurances that solutions will be found.

There are about 160,000 Christians in Israel and 14,000 in East Jerusalem.

According to The Times of Israel, Christians in Israel are becoming increasingly afraid after recent attacks by Jewish extremists on churches.

In a statement released online, Christian Schools in Israel said they had been offering their educational services to the children of the Holy Land from all faiths and denominations for centuries. The organisation also claimed that primary school teachers were no longer being allowed to take part in official teacher training courses.

The churches and monasteries that own these schools have developed the school buildings and facilities and strengthened the educational and moral message based on the love of God and man. The schools have been categorised for decades as "recognised and unofficial" schools in Israel and with partial funding from the education ministry.

However, the organisation has rejected an offer from the ministry to upgrade to "official" or "special" schools, even though this would bring them into the state system and guarantee 100 per cent of their budget, while allowing them to retain their special characteristics.

Christian Schools in Israel fear that Christian education in the Holy Land could die out altogether if more funds are not allocated.

Parents, who give more than $1,000 a year per child to the schools, have previously appealed to Pope Francis to lobby the Israeli government on their behalf.