Segregation, security and customer service have all been blurred in this week’s flurry of reports over the new separate bus services into Israel for West Bank Palestinian workers.

The new lines, which serve Palestinians working in Israeli cities, began operating on Monday amid accusations by human rights groups that they were being run on a racial basis, and counter-claims by the authorities that they were offering a much better service for the Palestinian passengers.

The bus line fracas is a reflection of changing circumstances in the West Bank where, due to the improving security situation, thousands of Palestinians have received permits to work in Israel, mainly in construction.

However, no comprehensive transport arrangements were made. In their absence, the workers were forced to catch buses originating in the settlements or pay what, for them, are huge sums to private taxi companies.

The tender for the new lines was issued by the Transport Ministry following complaints by Jewish local council leaders in the West Bank, who claimed that the Palestinian workers travelling on Israeli bus routes were “a security risk”.

They raised the concern that the buses connecting the settlements and the Tel Aviv region could be used by terrorists.

So far, two new bus routes starting from a central checkpoint in Samaria have begun operating and, while the Palestinians are still officially allowed to travel on the lines operating between the settlements and Tel Aviv and other coastal cities, according to Israeli human rights groups, most of these buses have now been stopped and Palestinians are forced to dismount and take “Palestinians-only” buses instead.

Israeli officials insist, however, that the new routes are not a form of segregation. Ben-Hur Achvot, the director of the company operating the routes, told Yediot Ahronot: “It is a plan that benefits the Palestinians and saves money they would have to pay in exorbitant fees to private taxi drivers.”

The Transport Ministry said: “These are not segregated routes for Palestinians but two designated routes aimed at improving the service for Palestinian workers entering Israel.”

The Ministry also said that the new routes had been launched “in co-operation with Palestinian organisations”.

Even so, it seems clear that the complaints about security by settlers having to travel alongside Palestinians was the original motive for setting up the new bus routes. On the other hand, the new routes are more convenient for many Palestinian workers and do save them money. This is the aspect that Israeli authorities have emphasised.

“This was a classic case in which no one had any idea of how this story would play in the media,” said one Israeli official this week. “Now it is too late for us to claim that the new lines are good for the Palestinians.”