Family and friends of the seven missing crew members have been fundraising to keep the search alive after the official operation ended on July 4.
Mr Funnell said the money had run out and it was unclear how the search would be funded after today.
"There are people trying to provide money but as far as the operator of the aircraft is concerned, the money that has been pre-paid to him has run out."
The Nina left the Bay of Islands on May 29 and was headed for Newcastle, Australia. Neither the yacht nor the seven people on board have been seen or heard from since June 4. The yacht is owned by professional captain David Dyche III, 58, and his wife, Rosemary, 60. They were on board with son David Dyche jnr, 17, and fellow Americans Evi Nemeth, 73, Kyle Jackson, 27, and 18-year-old Danielle Wright. Also on board was Briton Matthew Wootton, 35.
Mr Funnell said today's search would go until about 5.30pm.