But a spokesman for Health Minister Yaakov Litzman told AFP that his party of Torah Judaism would remain in the governing alliance "at this stage", preserving Netanyahu's meager majority in parliament at least for the time being.
Similar disputes have caused The crises of the Israeli coalition in the past, but Netanyahu was looking for ways to avoid further consequences.
"I resign from my cabinet position as health minister," Litzman wrote in his resignation letter, a copy of which was sent to AFP.  "The decision follows the public works carried out on Saturday by the railways of Israel," he added.
"I can not bear the ministerial responsibility for the grave damage to one of the eternal values of the Jewish people, which is the Sabbath."
Netanyahu, head of the right-wing Likud party, said he regretted Litzman's decision and signaled that he wanted to avoid calling new elections.
"The national government headed by the Likud is the best for the state of Israel," he said at the start of a cabinet meeting.
"I think every member of the coalition has an interest in its continued existence, I do not think so, I know"
Litzman will retain his seat in parliament.
The dispute is about rail maintenance work, which is less disruptive for travelers on Saturday, when there are no trains.
The national railway company says that some sabbaticals are necessary in the interest of public safety and to avoid congestion on the roads.
Litzman says it's fake "
" I regret that Israel Railways recently made the National Day of Sabbath maintenance, "he told Israeli army radio after giving his resignation to the cabinet secretary.
] "It unnecessarily does all the railway maintenance work on Saturday," he said.
Saturday begins at sunset on Friday and ends at dusk on Saturday.
Netanyahu has reportedly tried to persuade Litzman so that he does not resign offering support for various measures …
The ultra-Orthodox parties have often played a leading role in Israeli politics.
They control 13 seats in Netanyahu's coalition, which has 66 of 120 seats in parliament.
They demand strict adherence to Jewish law, particularly on the Sabbath, when work is not allowed, electricity must not be turned on or off, and The motors should not be operated between the sunset on Friday and the sunset on Saturday.