Thousands of children could be turned away from school in a new wave of strikes.

Union leaders confirmed talks with council bosses over a pay deal for school support staff had broken down.

The GMB and Unison unions will ballot for industrial action after the Easter holidays.

Their members have indicated they are overwhelmingly in favour of a walkout.

If no resolution is reached strikes will be staged within weeks, probably in late May.

The unions predicted all schools with workers involved would be forced to close.

The dispute involves more than 200 people working for 16 faith schools in Brighton and Hove who have been excluded, on a technicality, from payouts of up to £25,000 that have been made to their equivalents at non-faith schools.

Mark Turner, GMB branch secretary for Brighton and Hove, said: “We have asked Brighton and Hove City Council to address this situation but they have chosen not to. We are now facing industrial action and a disruption to the education system that nobody wants.”

The council is in the process of redressing a historical imbalance in the amount paid to unskilled workers in different departments, forced by equalities legislation introduced in 2003.

Staff have been able to claim compensation for being underpaid in comparison to others with the same abilities.

In many cases this has meant workers in schools, libraries and elsewhere have compared themselves with binmen, who are unskilled but have relatively high wages.

In the past few weeks the council has made “single status” pay-outs to hundreds of workers, including teaching assistants, cleaners and office staff at the city’s non-faith schools.

However, no offers have been made to their equivalents at the Catholic and Church of England schools because they are technically employed by their governors – even though the funding comes from the council.

Those workers are furious at the situation and regard it as an insult because they have always accepted pay restructuring in line with the other city schools.

Mr Turner said: “For most of them it’s not about the money, although they’d obviously welcome it. They are upset at the way they have been treated. They have been loyal to the council, and in some cases have accepted pay cuts when restructuring was carried out in 2005, and now it seems like the council is pulling a trick on them.”

One Catholic school teaching assistant, who asked not to be named, said: “We will be going on strike, there’s no doubt about it. What they have done is hugely unfair.”

Senior staff who oversee the faith schools for the Arundel and Brighton Catholic diocese and the Chichester Church of England diocese are also reported to be angry money will be deducted from their budgets to fund the council’s payments despite their workers missing out.

The dispute involves staff at 15 primary and junior schools and Cardinal Newman Catholic School – the largest secondary in Brighton and Hove, with more than 2,000 pupils. They make up a quarter of the city’s 64 schools.

The strikes would be the second time in just over a year industrial action has forced closures, following a teachers’ pay row in April 2008.

Two more days of classes were lost when snow closed the city’s schools in February.

A council spokesman said: “We cannot make single status offers to staff at faith schools simply because they are not employed by the council.

“We are aware of all the potential issues surrounding this situation and we have taken them into account.”

He said 93% of those offered pay-outs had accepted them.

Those who have not can either return to accept the offer or mount legal challenges for higher payments.

The unions said there were about 1,000 workers, including those at faith schools, who had not been offered a payment on technicalities.

They are preparing legal test cases to challenge the system.