Qatar has admitted for the first time that it sent hundreds of troops to support the Libyan rebels who overthrew Muammar Gaddafi's regime.

The Gulf state had previously acknowledged only that its air force took part in Nato-led attacks.

The revelation came as Qatar hosted a conference on the post-Gaddafi era that was attended by the leader of Libya's ruling National Transitional Council, Mustafa Abdel-Jalil, who described the Qataris as having planned the battles that paved the way for victory.

Abdel-Jalil also said he was asking Nato to extend its mission beyond the end of the month, when it had been due to end, until the end of the year. Help was needed because regime loyalists posed a threat from neighbouring countries, he said.

Gaddafi relatives and other key figures have fled to Algeria and Niger, amid speculation about the whereabouts of the deposed leader's son Saif al-Islam.

A Libyan military official with the NTC told Reuters that Saif and the former intelligence chief Abdullah al-Senussi are proposing to hand themselves in to the international criminal court. A spokesman for the ICC, however, said it had received no confirmation of the claim.

The Associated Press meanwhile reported an adviser to Niger's president, Mahamadou Issoufou, as saying Senussi was in their country.

It also has emerged that now the fighting is over, Qatar is to lead international efforts to train the Libyan military, collect weapons and integrate often autonomous rebel units into newly established military and security institutions – seen by the UN and western governments as the key challenge facing the NTC.

Qatar played a key role in galvanising Arab support for the UN security council resolution that mandated Nato to defend Libyan civilians in March. It also delivered weapons and ammunition on a large scale – without any clear legal basis.

There were repeated rumours about and occasional sightings of Qatari special forces in Libya during the war. Until now, however, there had been no official confirmation of actions that were not explicitly authorised by the UN.

The Qatari chief-of-staff, Major-General Hamad bin Ali al-Atiya, said: "We were among them and the numbers of Qataris on the ground were hundreds in every region. Training and communications had been in Qatari hands. Qatar … supervised the rebels' plans because they are civilians and did not have enough military experience," AFP quoted him as saying. "We acted as the link between the rebels and Nato forces."

Qatar, whose gas reserves and tiny population make it one of the richest countries in the world, has long pursued an activist foreign policy, promoted by al-Jazeera, the Doha-based satellite TV channel.

But there was still surprise when it sent most of its air force to join Nato's operation and delivered large quantities of what were described as defensive weapons but which included Milan anti-tank missiles to the rebels.

Qatari special forces are reported to have provided infantry training to Libyan fighters in the western Nafusa mountains and in eastern Libya. Qatar's military even brought Libyan rebels back to Doha for exercises. And in the final assault on Gaddafi's Bab al-Aziziya compound in Tripoli in late August, Qatari special forces were seen on the frontline. Qatar also gave $400m to the rebels, helped them export oil from Benghazi and set up a TV station in Doha.

Libyan gratitude is clear. The maroon and white flag of Qatar is often flown at celebrations and Algeria Square in central Tripoli has been renamed Qatar Square in honour of the country's support in toppling Gaddafi. Some, however, express concern at the emirate's support for Islamist elements such as the 17 February Martyrs Brigade, one of the most influential rebel formations, led by Abdel-Hakim Belhaj.

Ali Salabi, an influential Libyan Islamist cleric, lived in exile in Qatar for years before this year's revolution. For some analysts the emir's strategy is to support democratic forces selectively in the Arab world, partly to improve the country's international standing while diverting attention from the Gulf, where anti-regime protests have been crushed in Bahrain and bought off in Saudi Arabia.