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The Saudi minister of Islamic affairs has sparked anger online after he praised Israel for allowing pilgrims to travel to the kingdom for the annual hajj pilgrimage.

Abdel Latif Al-Sheikh made this week during the hajj pilgrimage, while accusing Qatari authorities of preventing their citizens from attending the religious rite.

"What is astonishing is the state of Israel, with all that we know about it, has not prevented Muslims from coming to the kingdom to perform their religious duty," al-Sheikh said.

"However, another country has banned pilgrims. This is a serious mistake… whoever does such a thing is liable to be punished by God," he added, in a thinly veiled reference to Doha.

Israeli authorities were quick to thank the minister for his praise.

"Thank God, Israel has facilitated the travel of over 4,000 Muslim citizens in the country.. to perform hajj," the Israeli government's Arabic-language Twitter account said on Tuesday.

The minister's comments have angered many social media users, who accused the religious official of "normalising" relations with Israel.

Other Twitter users slammed the Saudi government for its "warming ties" with the Jewish state.

The praise for Tel Aviv comes amid the worst political crisis to grip the Gulf, pitting Saudi Arabia against Qatar.

Qatar has accused Saudi Arabia of barring its citizens from this year's hajj, which took place this week.

Around 1,200 Qataris were eligible to perform hajj under a quota system but Qatar said it has become impossible to obtain permits.

Qatar's National Human Rights Committee said Saudi Arabia shut down an electronic system used by travel agencies to obtain permits for Qatari pilgrims.

Saudi authorities have claimed Qatari pilgrims were allowed into the kingdom for the hajj.

A Saudi-led bloc of Arab countries accuses Doha of cosying up to both Sunni Islamist extremists and Shia Iran, Riyadh's main rival.

They have cut all ties with Qatar - which denies the charges - and banned all flights to and from Doha.