The cancellations affected 150,000 passengers out of a daily total of 213,000, the country's rail company said, leading to replacement shuttle buses and gridlock on roads.
Israeli Prime Minister Benjamin Netanyahu cancelled rail work set to be undertaken over Sabbath, the weekly Jewish day of rest from sundown Friday to sundown Saturday, after objections from ultra-Orthodox Jewish parties.
Ultra-orthodox parties, which demand strict adherence to Jewish law, hold key positions in Netanyahu's government and have often played a kingmaker role in Israel's politics.
Hit by the Sabbath ban, trains between the northern city of Haifa and commercial capital Tel Aviv could not run today morning, the start of the working week in Israel.
More From This Section
The work instead began after sunset yesterday, with the train service only resuming today evening after the rush-hour peak.
Soldiers set to return to their bases after the weekend were reportedly among those affected by the morning cancellations, with special buses arranged for their transport in response.
Several hundred people protested in Tel Aviv and Haifa yesterday at the disruptions, media reported.
He argued that Katz had no reason to order the work to go ahead over Sabbath.
"This crisis is completely unnecessary," Netanyahu said at the start of a cabinet meeting today.
"Ministers are named to avoid crises, not to create them."
The two men have frequently jousted and speculation has built over whether Netanyahu will fire Katz, who receives support from a key faction of Likud.
But after a snap poll for Israeli public radio today showed 80 percent of the public against such a move, with 43 percent of respondents fingering Netanyahu as mainly to blame for the uproar, media reports said Katz's job was no longer on the line.