Libya must urgently secure weapons hoarded by the Gaddafi regime amid growing fears that smugglers are exploiting the chaos there to loot hundreds of portable missiles and other small arms, western officials have warned.

The US and Nato are pressing the National Transitional Council to make the issue a priority because of concerns that the trade has already begun, with reports that some African mercenaries who fought for Colonel Muammar Gaddafi are returning home laden with weapons.

One anxiety is that Gaddafi's remaining stockpile of shoulder-launched missiles could end up in the hands of terrorists.

The UK's National Security Council raised the issue with Libyan rebels in March and the Guardian understands that US officials based in Benghazi are now taking a lead in helping to identify where the caches may be, and how best to protect them. The UK and France have special forces in Libya, but officials would not be drawn on whether the soldiers are now involved in anti-smuggling operations.

In a private meeting with NTC leaders at the Friends of Libya summit in Paris, the US secretary of state Hillary Clinton said the safety of the Gaddafi's weapons was "an urgent security priority facing Libya and the broader region".

A Nato official added: "The risk of seeing weapons reaching members of terrorist organisations is always a concern. We know from experience that extremists and terrorists can take advantage of instability and lawlessness. We should do our utmost to avoid that situation. We expect all sides to maintain accountability of weapons."

A British spokesman said: "The issue of proliferation in Libya has been a priority for the National Security Council since this crisis began."We have raised it with the NTC at regular intervals to ensure that weapons are secured and monitored the situation closely."

The Guardian has spoken to a number of NGOs and independent observers who believe that scores of weapons from the Gaddafi arsenal have already disappeared and that the trade presents a potential threat to the region.

Fred Abrahams of Human Rights Watch, who is in Tripoli, said anti-tank missiles were among weapons looted by Libyans before anti-Gaddafi militias overran western towns. "There are reports of Libyans picking up anti-tank missiles like ants. Every second Libyan has arms. The UN should be thinking of a decommissioning programme, a buy-back programme."

Abrahams said concern was not only about the number of missiles, including Grad truck-mounted rockets, but what he called "standard bullets and bombs" – equipment that could be used to make improvised explosive devices, widely deployed by insurgents in Afghanistan.

Early in the six-month conflict, thousands of 122mm Grad rockets were reportedly found in abandoned bunkers in eastern Libya.

British officials say they are concerned in particular about heatseeking man-portable air defence systems (Manpads), such as SA7 shoulder-fired surface-to-air missiles, getting into the wrong hands. Though most military aircraft are now equipped with countermeasures, civilian planes are not. Helicopters remain vulnerable to rocket-propelled grenades, officials said.

Referring to reports that anti-Gaddafi rebels have been selling arms, Matt Schroeder, director of the arms sales monitoring group at the Federation of American Scientists in Washington, said this was "feasible and plausible … weapons may have been trafficked".

The US has promised $4.5m (£2.8m) to collect and destroy Libya's missiles and other light weapons, according to the congressional research service and state department.

Officials in Mali confirmed last week that a leader of the country's last Tuareg rebellion had been killed on his way back from fighting for Gaddafi. Though the circumstances were confused, Reuters quoted a military official in Mali saying that Ibrahim Ag Bahanga was killed as he smuggled weapons across the border from Libya. "He had got his hands on lots of weapons in Libya … and he hid them on the border with Algeria and Niger," the official said.

US officials were reported as saying that a small number of Soviet-made SA7 missiles from Libya had reached the black market in Mali, where al-Qaida in the Islamic Maghreb has been active. Other regional governments fear that the region could become even more lawless due to an influx of weapons and fighters from Libya's conflict.

Earlier this week, Algeria's foreign minister said his government was certain that al-Qaida's north African affiliate had obtained weapons on the black market that flourished during the Libyan civil war.

Mourad Medelci said countries across North Africa had seen proof "on the ground" that al-Qaida in the Islamic Maghreb had taken advantage of instability in Libya to procure weapons with which to expand its campaign of terrorism.

"It's not just a worry or a feeling, it's a certainty," Medelci told French radio.

He said that Libya was vulnerable to terrorists taking refuge within its borders and using the country as a springboard for terrorism throughout the region, AFP, the French news agency, reported.

Pieter Wezeman of the Stockholm International Peace Research Institute, Sipri, which monitors the arms trade, said Gaddafi imported hundreds of French-made Milan guided missiles and Russian SA 24 missile launchers adding to an arsenal which included some 20,000 older short-range surface-to-air missiles.

"Many of those, we know, are now not accounted for, and that's going to be a concern for some period of time," General Carter Ham, head of the US military's Africa Command, told the Senate armed services committee in April.

The British government approved the sale to Libya of equipment including guns and small-arms ammunition valued at more than £200m over the first nine months of last year, according to the latest figures compiled for the Foreign Office. In 2007–2008 Ukraine supplied more than 100,000 rifles to Libya.