A decision on funding next year's $100,000 campus-wide roll-out of the scheme - designed to build bridges between students and city residents while providing a healthy alternative to excessive student drinking - was to be made last month, Mr Thomson, director of Christian group Student Life, said.
But that deadline passed without communication from the pilot scheme's other partner organisations - the city council, the Otago University Students Association (OUSA), and University of Otago, he said.
He is concerned financial constraints faced by the city council and the uncertain future of the OUSA may mean those organisations, the university, and the Department of Internal Affairs might decline applications to fund the scheme next year.
"We want to be able to do, with these organisations, what we've set out to do together," Mr Thomson said.
"Unfortunately the OUSA is in dire straits, the city council finds itself in the same predicament financially, and a protracted discussion with the university is proceeding at a snail's pace.
"It's sad because the Scarfie Card would benefit everyone."
Last month it was confirmed the city council faced an annual $8 million shortfall in dividend payments from its companies.
OUSA has also been attempting to cut costs in the face of likely revenue reductions if Parliament adopts the Voluntary Student Membership (VSM) Bill, which would remove compulsory membership of student associations.
A $25,000, 10-week pilot of the Scarfie Card scheme was run between March and mid-May, funded by OUSA, the city council, the university, the Bank of New Zealand and Alcohol Advisory Council of New Zealand.
Of 786 students targeted in the pilot, 8% completed volunteer tasks requested by members of the public.
"If this 8% was applied to the whole of the university population it would result in 1600 students taking part in volunteer work," Mr Thomson said.
"The direct benefit to the city at minimum wage levels is $343,000 a year.
"That beats the pants off what's happening without the scheme."
The scheme was "of strategic benefit" to the university and the city because "it touches on key areas both are concerned with", he said.
"Meanwhile time ticks on and Scarfie Card is coming close to missing deadlines to run next year.
"To lose the scheme simply consigns students back to their ghetto ... where they are destined to repeat another year of alcohol-fuelled recreation."
The Star approached the university, OUSA and the city council to ask whether they still supported the Scarfie Card scheme and whether funding would be provided for the 2012 roll-out.
In a written statement, a university spokesman said the university had not yet made a final decision regarding the funding request.
OUSA president Logan Edgar said the association supported the scheme in principle but "on a financial level we can't commit to anything with VSM looming".
Dunedin Mayor Dave Cull said it was "an ambitious project with an ambitious budget".
The council was "waiting for some direction from the university", which Mr Cull understood was still in discussions with Mr Thomson.