The Commons has rejected proposals to keep protections for child refugees in the redrafted EU withdrawal agreement bill, triggering dismay from campaigners.

Alf Dubs, the Labour peer who successfully campaigned for this protection for refugee children in 2016, said it was a “very depressing” development.

“It is very disappointing that the first real act of the new Boris Johnson government is to kick these children in the teeth. It is a betrayal of Britain’s humanitarian tradition and will leave children who are very vulnerable existing in danger in northern France and in the Greek islands,” he said.

MPs voted 348 to 252 against the amendment, which had previously been accepted by Theresa May’s government and which would have guaranteed the right of unaccompanied child refugees to be reunited with family members living in the UK after Brexit.

Dubs, whose campaigning work on this issue was inspired by his experience of being welcomed to Britain after fleeing the Nazis on the Kindertransport, said he would continue to fight for the rights of refugee children in the House of Lords next week.

As all amendments to the government’s proposed Brexit bill failed under the weight of the Conservative party’s majority, Downing Street sought to address concerns of MPs on a range of issues. Following the vote, Downing Street insisted that the commitment to child refugees had not been abandoned, but had just been removed from the Brexit withdrawal agreement bill “so it delivered on what it was designed to do”.

Johnson’s press secretary said the provisions as set out in the Dubs amendment would remain government policy, but that there was not a need to set this out as a specific negotiation strand in the withdrawal agreement bill.

“Protecting vulnerable children will remain our priority after Brexit, and this new clause [on refugees in the bill] reaffirms our commitment, while clarifying the role of parliament and government in the negotiations,” he said.

In Scotland, in a largely symbolic exercise, the Holyrood parliament voted to comprehensively reject the UK government’s EU withdrawal bill, after the Scottish government urged MSPs to withhold consent from legislation it described as “uniquely offensive to Scottish democracy”.

Reflecting the increasingly fractured relationship between the Scottish and UK governments, the vote came as the new intake of SNP MPs at Westminster pressed their case for a second independence referendum at prime minister’s questions earlier on Wednesday.

The Scottish government’s Brexit secretary, Michael Russell, told MSPs on Wednesday afternoon: “England and Wales voted to leave and are leaving. Northern Ireland will have its own arrangements for a closer alignment and the right to decide their own future. Scotland alone of the four nations voted to remain but is being forced to leave with no special arrangements or say over its future relationship with the European Union.”

Referring to changes made by the government to the most recent version of the bill, Russell said it was “inexplicable” that protections for child refugees had been removed, adding that he had no confidence that the UK government would improve workers’ rights via a separate bill as has been promised.

The Scottish and Welsh parliaments have voted against giving legislative consent to the withdrawal agreement previously, although, because they cannot prevent any UK legislation from becoming law, this has been a largely symbolic exercise.

Meanwhile, Northern Ireland businesses have vowed to continue their fight for a Brexit mitigation package after the government ruled out changes to upcoming laws to protect them.

A cross-party attempt to get an amendment in the House of Commons on Wednesday was rejected by 75 votes.

“The fight will go on in the House of Lords, at committees and with the EU. We are determined to protect NI families and the affordability and choice they enjoy,” Aodhán Connolly, the director of the Northern Ireland Retail Consortium, said in a statement.

“The amendment to the bill may have failed to be passed … but a stark warning has been raised that this current protocol will have damaging effects for our households and economy. The narrative that Northern Ireland is sorted has been broken.”

The row over Northern Ireland intensified in October when it emerged that there would be a trade barrier down the Irish sea to prevent a border with the Republic of Ireland.

While Johnson has been accused of misleading the public by insisting there will be no checks, the Northern Ireland minister, Robin Walker, admitted on Wednesday there would be some “reporting requirements” on goods from Great Britain to Northern Ireland supermarkets, factories and elsewhere because of Brexit.

But he said the government would use a joint committee of EU and UK representatives “to reduce those [checks] and make sure we have the absolute minimum burden” for businesses.

A group of cross-party MPs had tabled an amendment that would have guaranteed a 12-monthly assessment of the impact of Brexit and compensation for businesses if the impact was adverse.

The DUP MP Sammy Wilson said the demands were “reasonable” given that Northern Ireland would be treated differently to the rest of the UK.