Spain’s acting prime minister, Pedro Sánchez, is on the verge of securing another term in office after his socialist party won the support of Catalan separatists by offering a deeply controversial amnesty for those who took part in the illegal and failed bid for regional independence six years ago.

The deal between the Spanish Socialist Workers party (PSOE) and the centre-right Junts (Together) comes after a week of tense negotiations and amid widespread concerns over the amnesty, which have led to street protests, dire warnings from conservative judges and questions from Brussels.

Speaking shortly after the agreement was announced, the PSOE’s organisational secretary, Santos Cerdán, said the negotiations had yielded “a historic opportunity to resolve a conflict that could – and should – only be resolved politically”. He said the proposed amnesty bill would now be put before parliament, adding that a new, socialist-led government would offer a progressive alternative to an alliance between the conservative People’s party (PP) and the far-right Vox party.

The deal follows months of uncertainty caused by an inconclusive snap general election in July, in which the PP narrowly beat the PSOE. But the PP failed to muster the support it needed to form a government with Vox, leaving the way clear for the PSOE and its allies in the leftwing Sumar alliance.

To cobble together the necessary parliamentary support, however, Sánchez has been forced to rely on the support of smaller parties, including the two main Catalan pro-independence parties, the Catalan Republican Left (ERC) and Junts.

Both Catalan parties made their support conditional on an amnesty for all those who had taken part in the bid for independence – including the Junts leader, the former Catalan regional president Carles Puigdemont, who fled to Brussels to avoid being arrested for masterminding the attempt to secede.

Although Sánchez now has the backing of both the ERC and Junts – meaning he can attempt an investiture as soon as next week – the proposed amnesty law has infuriated the Spanish right and angered many traditional socialist voters.

A poll in mid-September showed 70% of Spaniards opposed an amnesty, and about 200,000 people have taken part in three large, recent rallies against the measure organised by the PP and Vox.

Efforts to close the deal with Junts had suffered a setback on Monday, after a judge at Spain’s highest criminal court, the Audiencia Nacional, announced that Puigdemont and other separatists were being investigated as part of a probe into the actions of the secretive pro-independence platform Tsunami Democràtic.

The judge alleged that Puigdemont had played a leadership role within the platform whose actions – such as closing roads and blockading Barcelona airport in October 2019 – “could be classified, in a preliminary way, as terrorism”. Any possible terrorism charges would not be covered by the amnesty.

Puigdemont’s legal team and advisers have dismissed such allegations as part of the “lawfare” being waged against the former regional president.

On Tuesday night, 39 people, including 30 police officers, were injured amid continuing protests against the amnesty outside the PSOE’s Madrid headquarters.

The demonstration, which was attended by Vox members and by fascist and neo-fascist groups, led to skirmishes between protesters and riot police, who responded with teargas and baton charges.

Video footage of the event – which was attended by about 7,000 people – showed some participants calling Sánchez a “criminal” and a “dictator”, and using a homophobic slur to refer to Spain’s acting interior minister, Fernando Grande-Marlaska, who is gay. It followed three much larger, peaceful protests that were called in Madrid and Barcelona by the PP and Vox, and which were collectively attended by a total of about 200,000 people.

On Wednesday, the EU justice commissioner, Didier Reyners, wrote to the acting Spanish government asking for more details of the proposed amnesty law, adding that the issue had raised “serious concerns” and had become “a matter of considerable importance in the public debate”.

In a polite but blunt reply, the acting government pointed out that the Spanish constitution did not allow caretaker administrations to put legislation before parliament. Any such legislation, it added, would be proposed by political parties. It did, however, offer to provide more details to the commission if and when the amnesty bill was tabled.

On Monday night, the conservative-dominated General Council of the Judiciary, the body that appoints top judges, warned that the mooted amnesty could lead to “the degradation, if not abolition, of the rule of law in Spain”.

Their warning came days after the Professional Association of Magistrates – a conservative group that represents most of the country’s judges – claimed the move was “the beginning of the end of democracy” that would “destroy the rule of law”.

Although the ERC and Junts have seized on the proposed amnesty as a means of reviving the stalled regional independence movement they are competing to represent, support for an independent Catalonia has plummeted in recent years.

At the height of the crisis in October 2017, a survey by the Catalan government’s Centre for Opinion Studies found 48.7% of Catalans supported independence and 43.6% did not. According to a survey conducted in July by the same centre, 52% of Catalans now oppose independence and 42% are in favour.