Occupied Jerusalem: Prime Minister Benjamin Netanyahu suspended on Wednesday new bus travel and checkpoint regulations for Palestinian labourers only hours after they were imposed to an outcry by critics accusing Israel of racial segregation.

Effectively overruling his defence minister, Netanyahu froze the edicts ahead of a meeting later in the day in Occupied Jerusalem with Federica Mogherini, foreign policy chief of the European Union, a group highly critical of Israeli policies in the occupied West Bank.

Netanyahu drew accusations at home and abroad of racism two months ago when he warned on election day that Palestinian citizens were voting in “droves”. He later apologised to members of Israel’s Palestinian minority for the remarks.

The “transit point programme” that began early on Wednesday would have required Palestinians labourers in Israel to return to the occupied West Bank at the end of the workday via one of four checkpoints, where they would be registered. They would have needed to use Palestinian-only buses to get there.

Israeli civil liberties groups objected, as did Palestinian officials and Israeli legislators, including several from Netanyahu’s right-wing Likud party and the leader of the opposition, Isaac Herzog of the centre-left Zionist Union.

“The segregation on public transport in Judea and Samaria is a needless humiliation, a stain on the country’s face and citizens,” Herzog said on Twitter, using the Biblical names for the West Bank area.

One Israeli official said the plan stemmed only from a need to “monitor the entry and exit of labourers who are not citizens, for security reasons, as any normal country would do”.

But as criticism of the move echoed in the Israeli media, a Netanyahu aide said the prime minister viewed the proposal as unacceptable.

“He spoke to the defence minister and it was decided to freeze it,” the aide said.

The now-suspended Defence Ministry initiative followed the opening in 2013 of Palestinian-only bus lines in the West Bank that ran in parallel to buses primarily serving Jewish colonists.

Hussain Fuqahaa, of the Palestinian Workers Union, said 45,000 to 50,000 Palestinians have Israeli employment permits.

He said an almost identical number work in Israel without them, and he described the travel restrictions as a “racist measure” taken under the pretext of security.