Concern is growing within Israeli and Western intelligence services over the role of the radical Muslim organisations connected to the Muslim Brotherhood in leading the armed uprising in Syria.

Free Syrian Army commanders interviewed recently by The Times claimed that the IHH, a Turkish humanitarian relief organisation, was involved in supplying fighters in Syria with arms. The IHH helped organise the flotilla from Turkey to Gaza in May 2010 in which nine activists were killed after violently opposing Israeli naval commandos commandeering the Mavi Marmara boat.

IHH is known to have ties with the Islamist administration in Ankara headed by Prime Minister Recep Tayyep Erdogan. Part of a network of Muslim Brotherhood-affiliated groups, it has been outlawed in Germany for allegedly funnelling financial donations to Hamas. IHH has been designated an illegal organisation by Israel.

The Times article claimed this week that IHH helped organise a ship carrying arms to Syria from Libya. It was alleged that the arms were distributed to Muslim Brotherhood fighters in the Free Syrian Army.

Syrian society is predominantly secular but the Muslim Brotherhood, though persecuted ruthlessly in the past, remains the only well-organised party within the Syrian opposition.

Around a quarter of the members of the Syrian National Council (SNC) are identified as Muslim Brotherhood supporters and they control the SNC’s logistics branch. Thanks to its connections in Turkey, Muslim Brotherhood members have been able to control many of the supply lines across the border and operate within the refugee camps set up by the Turkish authorities.

Many observers believe one of the reasons for the Assad regime’s survival is that it is split into secular, Muslim Brotherhood and Salafist elements. It is also thought that the Brotherhood’s predominance is stopping many ordinary citizens, fearful of an Islamist takeover, from supporting the revolution.