A locksmith has said the service door was not fully locked at the apartment where a crusading Argentinian prosecutor was found shot dead, and investigators have revealed the existence of a previously unknown entry, as more questions arose over the death of the man who had accused the president of a cover-up in a terrorist car bombing.

Alberto Nisman, who was set to testify to Congress on his allegations that President Cristina Fernández de Kirchner conspired to protect Iranian officials blamed for Argentina’s worst terrorist attack, was found late on Sunday next to a .22-calibre handgun and a bullet casing on the floor of the bathroom of his flat in Buenos Aires.

Viviana Fein, lead investigator into Nisman’s death, said on Monday it appeared to be suicide and there were no indications anyone else was involved. The apartment’s door was locked from the inside and there were no signs it had been forced, she said.

But family and friends of Nisman immediately rejected the findings and protesters took to the streets demanding justice for the prosecutor who had spent 10 years investigating the 1994 bombing of a Jewish community centre in Buenos Aires that killed 85 people.

Details began trickling out that raise questions about the suicide hypothesis. No suicide note was found and a test of Nisman’s hand showed no gunpowder residue, though Fein said that might have been due to the small calibre of the gun.

Then the locksmith who opened the back door to give detectives access to Nisman’s home said it had not been properly locked, raising speculation about whether a killer might have entered or exited the 13th-floor apartment.

After testifying to investigators on Tuesday, the locksmith, who gave his name to journalists only as Walter, said he was called to let the authorities into Nisman’s apartment.

The front door had a keyless system so he entered through the service door. Authorities said Nisman’s mother had been unable to open the service door because a key was in the lock on the other side.

“The service door wasn’t closed. I simply pushed the key and entered in two minutes,” the locksmith said. He added that he was able to quickly open the door with the help of a hook. “It took me longer to pack up my things (tools) than to open the door. If someone entered or not, I don’t know.”

The official news agency, Telam, said detectives had found a third access to the home, a narrow passage holding air-conditioning equipment that connects to a neighbouring apartment occupied by an unidentified foreigner. They were investigating a seemingly recent footprint and fingerprint found inside.

Fein said the gun found beside Nisman was registered to another man, Diego Lagomarsino, described by officials as a colleague of Nisman, who had given it to him.

The death, and Tuesday’s release of Nisman’s full report, caused a crisis for the government, which scrambled to promise “maximum transparency and cooperation” in the investigation.

The report accused Fernandez and the foreign minister, Hector Timerman, of reaching agreement with Iran to avoid prosecution of eight Iranians, including former senior officials, charged with involvement in the bombing. He said that would open a lucrative trade in Argentinian grains and meat for Iranian oil.

In the end, Interpol never dropped its “red notices” for the arrest of five of the Iranians, and the government said trade with Iran had diminished in recent years.

Nisman called it “a criminal plan to erase at a stroke the serious accusations that weigh on the Iranian fugitives … something unprecedented and never before seen.”

The document did not appear to show direct or documentary evidence of a deal, but it did include wiretap transcripts of several people discussing such negotiations and saying the deal was approved by la jefa – Spanish for a female chief – and at the highest level.

The government dismissed Nisman’s allegations as “weak” and “baseless”, and Fernandez on Tuesday released a long message saying Nisman’s investigation was meant “to divert, to lie, to cover up and confuse” before a trial of former president Carlos Menem and other officials for a separate alleged cover-up of the bombing. Nisman, however, was the prosecutor in that case as well.

Nisman was appointed to his post in 2005 by the then president Nestor Kirchner, Fernandez’s late husband, after a bungled 10-year investigation launched under Menem that led to a trial in which all the defendants were found innocent.