Indonesian football players, fans and pundits reacted with anger and sadness on Thursday after Fifa pulled the Under-20 World Cup from the host nation weeks before it was due to kick off, following protests against Israel's participation.

The humiliating loss came after two influential governors advocated banning Israel from the competition.

Indonesia and Israel do not have formal diplomatic relations, and support for the Palestinian cause in the world's most populous Muslim-majority nation runs high, fuelling local opposition to hosting the Israeli team.

Fifa's decision to find a new host – thereby nixing Indonesia's automatic qualifying spot – puts the country's most popular sport back in the doldrums and facing another bout of isolation as it recovers from a stadium stampede that killed 135 people last year.

Some of the archipelago nation's football prodigies took to social media with fury and heartbreak after losing the chance to play in what Fifa bills as the "tournament of tomorrow's superstars".

"Energy, time, sweat, and even blood we have put in, but in a moment failed because of political reasons. Here's our big dream that you've destroyed," wrote 19-year-old striker Rabbani Tasnim.

An Indonesian football association video showed players with heads bowed and their coach in tears after receiving the news late on Wednesday that Fifa would seek a new host.

"We, the players, are now affected, not just us but all footballers," said 18-year-old striker Hokky Caraka.

Head coach Shin Tae Yong said he was "heartbroken" and "tired" after preparing the team for more than three years for the youth football showpiece.

President Joko Widodo said on Thursday he was "disappointed and saddened" by the decision but said Indonesia had to respect it.

On Thursday morning, flower boards for the players popped up outside the football association headquarters in central Jakarta, including one that read "do not give up on your dream".

Indonesians inundated the Instagram page of Central Java governor Ganjar Pranowo – one of the leading candidates in next year's presidential election – with negative comments after he opposed Israel's participation.

Bali governor Wayan Koster had also joined the anti-Israel chorus and around a hundred conservative Muslim protesters held an anti-Israel rally in Jakarta this month.

Koster on Thursday cited the occupation of Palestinian lands and "threat and security" concerns for rejecting Israel's participation, comparing his call for a ban to Russia's exile from the 2022 World Cup in Qatar, following Moscow's assault on Ukraine. (AFP)