The letters to Israeli government officials began piling up last year. Leaders of Jewish settlements in the northern West Bank, citing complaints by residents of harassment by Arabs on their daily commute, lobbied to restrict travel by Palestinian laborers using Israeli bus lines to get to and from their jobs in Israel.

An online petition posted by settlers from the town of Ariel demanded that Palestinians be barred from the buses, alleging that Jewish passengers were experiencing “frightening rides” and feared for their safety. Urging the authorities to act, Ariel’s mayor wrote that his constituents had been subject to abuse and “thuggish acts” by Palestinian passengers.

This week, Israel’s transportation ministry rolled out its solution: special bus lines that pick up Palestinian workers at a crossing point into Israel and return them there at the end of the work day.

The announcement, suggesting separate bus lines for Jews and Arabs, created immediate controversy.

The ministry said the new lines, which began operating at a crossing from the Israeli-occupied West Bank on Monday, are “meant to improve service for Palestinian workers” and replace unregulated vans whose drivers ferry laborers to their workplaces at exorbitant prices.

A police spokesman, Micky Rosenfeld, indicated that Palestinians would still be permitted to ride Israeli buses, but he said that if the buses are stopped for police inspections, Palestinian passengers would henceforth be “diverted” to the crossing point near the town of Qalqilya, where the new service is provided, “to make things more efficient and effective.”

Some Palestinian laborers welcomed the cheaper alternative, but it drew sharp denunciations from Israeli critics, who accused the authorities of institutionalizing ethnic separation on public transport that by law should be open to everyone.

“This is what apartheid looks like,” Zehava Galon, a lawmaker who heads the leftist Meretz party in parliament, wrote on her Facebook page. “Separate bus lines for Palestinians and Jews prove that democracy and occupation can’t coexist.”

In an editorial Tuesday, the liberal daily Haaretz denounced the new bus arrangement as “racist segregation,” saying it added another layer to a host of restrictions that discriminate between Palestinians and Israelis in the West Bank.

And Sarit Michaeli, spokeswoman for the Israeli human rights group B’tselem, which monitors conditions in the Palestinian areas, called the arrangement “an attempt to use security and convenience as a cover for racism.”

“We know from experience that you can’t have separate but equal,” she added. “Separation by definition is discriminatory.”

Responding to the critics, Transport Minister Yisrael Katz said he had given instructions to ensure that “Palestinians entering Israel can travel on all public transport lines in Israel, including all lines in Judea and Samaria,” a reference to the West Bank.

Katz’s spokesman, Avner Ovadia, said that the new bus service was prompted by crowding that has occurred on regular routes as more Palestinians have been permitted into Israel to work and that there were plans to increase the number of buses serving the laborers. More than 30,000 Palestinians from the West Bank have permits to work in Israel, according to the Israeli Defense Ministry. Many work in construction or factory jobs.

“All lines are open to everyone, and there is no separation between Jews and Palestinians,” Ovadia said.

Still, Palestinians and Israeli rights activists have reported repeated cases in which Palestinian laborers heading home on Israeli buses have been ordered off by police or soldiers, on the grounds that they had to return to the West Bank through specific checkpoints.

Ofra Yeshua-Lyth, an activist with the group Civil Disobedience, said that on Thursday she witnessed Palestinian passengers being ordered off three buses and told to walk to a checkpoint more than a mile away. She said reports of such incidents had increased in the past month.

Israel’s Channel Ten television on Monday broadcast footage of a Palestinian worker being refused entry to a bus, apparently by the driver, when he tried to board on his way to his job as a plasterer in Israel.

Rosenfeld, the police spokesman, confirmed that there had been cases in which Palestinian laborers were told to get off the Israeli buses and pass through checkpoints processing Palestinians, but he said most were escorted to those points by police officers.

Returning from work Tuesday, several Palestinians who stepped off a special bus bringing them back to the crossing point near Qalqilya welcomed the new service, which they said cost half of what they would have paid for transport in a privately driven van.

Bassam Hanani, 38, a father of four, said the new bus routes were safer “because we avoid the settlers,” who he said were hostile and used “foul language” against the Palestinians on the Israeli routes.

Naim Liftawi, 40, returning from a job in an upholstery factory in the town of Kfar Sava, said that by using the new transport service he avoided being ordered off buses by Israeli police and abuse from settlers, one of whom he said had once spit in his face.

As for the charges of apartheid, “they can say what they want, as long as I’m safe on the bus,” Liftawi said. “I just want to put bread on the table for my children.”

Sufian Taha contributed to this report.