Being a member of, or showing support for, Palestine Action will be a criminal offence from Saturday after a last-minute legal challenge to suspend the group’s proscription under anti-terrorism laws failed.

A ban on Palestine Action, which uses direct action to mainly target Israeli weapons factories in the UK and their supply chain, was voted through by parliament this week but lawyers acting for its co-founder Huda Ammori had sought to prevent it taking effect.

After a hearing at the high court on Friday, however, Mr Justice Chamberlain declined to grant her application for interim relief. Ammori said: “The home secretary is rushing through the implementation of the proscription at midnight tonight despite the fact that our legal challenge is ongoing and that she has been completely unclear about how it will be enforced, leaving the public in the dark about their rights to free speech and expression after midnight tonight when this proscription comes into effect.”

Chamberlain said: “I have concluded that the harm which would ensue if interim relief is refused but the claim later succeeds is insufficient to outweigh the strong public interest in maintaining the order in force.”

Ammori sought permission to appeal against Chamberlain’s decision in an 8pm hearing that lasted approximately one hour at the court of appeal on Friday night, in an attempt to prevent the ban coming into force. But at about 10.25pm – less than two hours before it was due to take effect – the three judges, led by the lady chief justice, Sue Carr, refused permission.

It means Palestine Action will become the first direct action protest group to be banned under the Terrorism Act, placing it in the same category as Islamic State, al-Qaida and the far-right group National Action.

Raza Husain KC, representing Ammori, described the proscription decision in the hearing before Chamberlain, as “an ill-considered, discriminatory and authoritarian abuse of statutory power”. He said it was “absurd” to label a civil disobedience direct action protest group that does not advocate violence as a terrorist organisation.

“The main target has been stopping Elbit Systems … which markets itself as the backbone of the IDF [Israel Defense Forces],” said Husain. “As my client says: ‘The aim of terrorism is to take lives and hurt people, that’s the opposite of what we do.’”

He said before making the decision the government had engaged with the Israeli government, Elbit Systems and pro-Israeli lobby groups, while Palestine Action and other pro-Palestine groups were not consulted.

Blinne Ní Ghrálaigh KC, also representing Ammori, said what was going on in Gaza was “an annihilation, it is a genocide” and Palestine Action was “seeking to disrupt and prevent” UK complicity in it.

Ben Watson KC, representing the home secretary, focused on the proscription procedure in his submissions. “All of these issues, all of that evidence is supposed to go to the secretaries of state… it’s only after that process, after the secretary of state has had a chance to consider … then the matter goes before Poac [the Proscribed Organisations Appeal Commission].”

He said only then could the case go to the court of appeal and then, potentially, the supreme court.

Watson said Palestine Action’s activities met the statutory test for proscription and that if the ban took effect but the group subsequently won a judicial review against proscription it would not cause “irreparable harm” to it.

He told the court that if a temporary block was granted, it would be a “serious disfigurement of the statutory regime”.

The protest group Defend Our Juries wrote to the Met police commissioner, Mark Rowley, on Friday to tell him that it “may be committing offences under the Terrorism Act” in Parliament Square from 1pm on Saturday. It said non-violent protesters would hold signs saying: “I oppose genocide. I support Palestine Action.” The letter said that they “refuse to be bystanders to what’s happening to the people of Palestine, who are bombed, starved and gunned down as they queue for food”.

Several hundred protesters gathered, waving Palestinian flags and carrying signs saying “Free Palestine” and “We are all Palestine Action” outside the Royal Courts of Justice.

UN experts, civil liberties groups, cultural figures and hundreds of lawyers have condemned the ban as draconian and said it sets a dangerous precedent by conflating protest with terrorism.

Another hearing is scheduled for 21 July when Palestine Action will apply for permission for a judicial review to quash the order. In the meantime, and unless the judicial review is successful, membership of, or inviting support for, the group will carry a maximum sentence of 14 years in prison.