Urgent efforts to secure anti-aircraft missiles from Libya after the fall of Muammar Gaddafi blinded western governments to the danger of other weapons going missing and fuelling conflicts in Mali and elsewhere, an expert says.

Reliable information about the source of arms being used by Islamist rebels in Mali is hard to come by, but much of it appears to come from Libya. In one striking case, Belgian-manufactured landmines originally supplied to Gaddafi's army appear to have been used by the jihadi militants who attacked BP's In Amenas gas facility in Algeria last week.

The US, working with Britain and France, focused on securing shoulder-launched anti-aircraft missiles, known as Manpads (man-operated portable air defense systems). Britain's Ministry of Defence said last year it had located 5,000 of an estimated 20,000 in Libya.

Peter Bouckaert, of Human Rights Watch, said his organisation had warned of the risks if Libya's conventional weapons were looted.

"From March 2011 these governments were solely focused on the Manpads," he told the Guardian. "We tried to get them to pay greater attention to other weapons but were unable to put them on their agenda. The Manpads were a very serious matter and you can imagine what a nightmare it would have been for the US or UK if one of their civilian planes was shot down by a Manpad that had gone missing in Libya when they supported the opposition."

Dyncorp, a US contractor, used former US special forces and CIA agents equipped with armoured vehicles and satellite communications to locate the missiles. "But when we tried to raise the need to take broader measures, their eyes glazed over and they said they were contracted to deal only with the Manpads," Bouckaert recalled.

Other weapons that went missing in Libya included anti-tank missiles, Grad missiles and mortars, some of which have been seen in Mali. Malian army officers have described being overun by heavily armed rebel forces equipped "just like Libya's army", with heavy machine guns on four-wheel drive vehicles, as well as anti-tank and anti-aircraft rockets and light weapons. Tuareg officers serving in the Libyan army brought the weapons with them after the fall of Gaddafi.

Algerian security officials warned as early as April 2011 that al-Qaida in the Islamic Maghreb had acquired surface-to-air missiles from Libya. "What we are seeing in Mali is one of the peripheral, spillover effects of the removal of Gaddafi," an EU diplomat said as the crisis escalated.

Libya closed its border posts with Algeria and its other neighbours in December but the central government in Tripoli still relies on local brigades and former rebel fighters with divided loyalties to maintain security in border areas.

"It takes a tiny fraction of the weapons missing in Libya to supercharge a conflict like Mali," said Bouckaert. "The arrival of new weapons changes the game. One day the rebels fight with AK47s and the next day they show up with anti-aircraft guns and other weapons and it's a completely different conflict.

"In a lot of these conflicts the focus is on the most exotic weapons, whether chemical weapons in Syria or Manpads in Libya, but we have to go back to Iraq in 2003 and look at the carnage caused by much more conventional weapons in the aftermath of the war.

"Two artillery shells can make a car bomb, and there are hundreds of thousands of them missing in Libya. For 10 years the US and its allies lost soldiers in Iraq to the weapons that they failed to secure in 2003, and now the same thing has happened on a more massive scale in Libya."