An Argentinian judge has refused to pursue allegations that president Cristina Fernández de Kirchner conspired with Iran to cover up the nation’s deadliest terrorist attack – raising the prospect of the case dying along with the prosecutor who presented it.

The accusation was made in January by Alberto Nisman, who less than a week after presenting the indictment was found dead with a bullet in his head.

In a nearly 300-page legal document he had claimed that the president, her foreign minister Hector Timmerman and other aides plotted to shift the blame for the 1994 bombing of the Amia Jewish community centre so that Argentina could secure access to Iranian oil.

The allegations shocked Argentina, which has already seen one former president, Carlos Menem, indicted for trying to subvert the course of justice regarding the attack, which killed 85 people.

But many analysts said Nisman’s case was flawed because it relied too heavily on intelligence from wiretaps and appeared to have been contradicted by events. Argentina has not boosted trade with Iran and the former head of Interpol has denied that its government has ever requested the lifting of “red notice” warrants against Iranian officials who were allegedly involved in the bombing.

A woman holds up flowers and a picture of late prosecutor Alberto Nisman on the route of his funeral procession. Photograph: Marcos Brindicci/Reuters

On Monday Judge Ariel Lijo declined to accept the indictment on technical grounds. Nisman had singled him out to handle the case, presumably because the judge was already investigating the earlier cover-up, but Lijo said the new accusations were beyond his jurisdiction.

Lijo said in a statement that “the mere fact it has some kind of link indirect or direct with the attack on the Amia, as in the present case” did not constitute sufficient grounds to tack Nisman’s charges on to the others.

A second judge – Daniel Rafecas – has also declined to take on the case, according to the domestic media, prompting several commentators to declare the indictment a poisoned chalice that nobody wants to accept.

The allegations will now move to a federal chamber, which will appoint a judge to oversee the investigation.

The lack of legal progress has done little to dent media speculation about the accusations and how they might be tied to Nisman’s death. Investigators have yet to determine whether the killing was suicide or murder.

President Fernández has denied Nisman’s claims and insinuated that his death is the responsibility of rogue agents from the intelligence agency who are trying to damage her reputation.