Counter-extremism thinktank's decision to ally itself with former EDL leader is viewed by many as a high-stakes gamble

For a few briefly awkward seconds last Tuesday, the press conference to mark Tommy Robinson's exit from the English Defence League was delayed, as his new-found Muslim allies in a counter-extremism thinktank struggled to open the door to the room of waiting television cameras and journalists.

It was an uncharacteristic glitch for Maajid Nawaz, co-founder of the Quilliam Foundation and a man frequently described as smooth and slick by those who have followed his public profile over the years since his transition from teenage gang member through to jailed Islamist extremist and, most recently, would-be Liberal Democrat MP.

However, senior figures working in the growing field of the study of counter-extremism and the rehabilitation of former extremists have been viewing its link-up with Robinson as a high-stakes gamble that has raised serious questions about the motivations of an organisation that has played a particularly controversial role.

If the latest accounts - for the financial year up to March 2012 - filed by the Quilliam Foundation are anything to go by, the high-profile injection of publicity also comes at a time when it may be facing challenging financial circumstances.

Two years after the Home Office began to wind down its funding for the organisation, those accounts show that Quilliam was facing mounting debts, while having little in the way of relative assets. Income from training, consultancy and publications were haemorrhaging, while its income from grants and donations fell from just over £900,000 in 2011 to £532,099 in 2012.

The company was in particular trouble in 2011, making a loss, but after taking radical action to cut back on expenses and parting company with half of its staff, it was just about able to make it into the red again in the following year, when Nawaz paid himself £77,438.

The situation is a far cry from Quilliam's earlier years, after its founding by Nawaz and Ed Hussain, another former Islamist who penned a memoir about his time in the radical Hizb ut-Tahrir (HT) group. Launched in a blaze of publicity, the group was the recipient of millions of pounds of government funding and backing from officials initially impressed with the group's embrace of anti-extremism.

According to a source familiar with its government ties, links eventually became frayed. "There was a sense that they just were not fulfilling their original remit. They had become flattered by Whitehall and Westminster, and were far too focused on producing reports and material that frankly was just not relevant to their actual aims and objectives, when what they should have been doing was countering extremism in communities.

"They also lacked credibility in the Muslim community. If you arrive at a meeting and are a former member of HT, people asked the question: 'Why should we listen to you when you were far too weak originally and you strayed into an extremist group. Why should you be rewarded now?'"

According to the same source, Quilliam's ties with government were not helped by the revelations that it had drawn up for British security officials a secret list which accused peaceful Muslim groups, politicians, a television channel and a Scotland Yard unit of sharing the ideology of terrorists.

Others in the field of counter-extremism studies and advocacy, meanwhile, voiced scepticism about how, around the time that its government funding was drying up, Quilliam appeared to be branching out into focusing on far right extremism.

"Some people feel that they have made a bit of a land grab for far-right extremism," says a senior figure at another organisation working in the sector.

"In 2010, when it began to look like Islamist extremism was slightly on the wane and there was an interest in far-right extremism, some people were slightly cynical that the Quilliam Foundation had originally said they were the specialists in Islamism but suddenly started to want to do work on far-right extremism as well. Some people feel that was a cynical land-grab to keep them in the media. But they are a thinktank that has to raise money and has to be visible."

On its website, Quilliam says it is funded by both private and public funds, adding: "Our ideas, projects, and output are all made possible by the support of private individual donations, private philanthropic foundations and trust grants, as well as public sector grants. All funding is accounted for responsibly, and we are externally audited annually. Specific details of Quilliam's finances are published in our annual report."

However, journalists who asked for a copy of the annual report this week were told by a press officer: "There is only one print copy and that that has gone missing."

The reaction of figures from Quilliam to those who raised questions about the Robinson link-up was also a sharp one. The foundation's head of outreach, Ghaffar Hussain, criticised "the usual coterie of trendy wine bar types" who had voiced sceptism about Robinson's departure from the EDL.

Hussain also took on the Nottingham University far-right expert Dr Matthew Goodwin, after he described Robinson's EDL resignation as "disingenuous nonsense" and suggested that the episode owed more to the quest for publicity than a genuine conversion, adding that "both the EDL and Quilliam have had their own difficulties in recent months".

Hussain tweeted to Goodwin that standards at Nottingham were "clearly slipping", adding: "I suppose your research grants will be harder now."

Quilliam did not respond to a series of queries from the Guardian.