In December, hundreds of doctors signed undated resignation letters because of funding concerns and workforce strain.
A rescue package, which would have increased training places, was then agreed with the health minister.
However, Dr Tom Black said that because of the uncertainty at Stormont, that deal is unlikely to be completed.
"Recent weeks have clearly shown that general practice here is on the edge of a full-blown crisis," said Dr Black. "It is catastrophic.
"Continued uncertainty over the budget means that plans we had worked hard to agree with the Department of Health to address the issues, and put general practice back on an even keel cannot now be implemented.
"A contingency plan is now urgently needed to address what should be done in the event of an election and further delays to a budget being agreed.
"The bottom line is that the only way to save the GP service at the moment is to leave the NHS," Dr Black added.
The rescue package is to be brought before BMA members on 25 January, when they will decide whether or not to stay in the NHS.
Health Minister Michelle O'Neill told the BBC that primary care was the bedrock of the health and social care system.
"It was agreed to invest up to Â£7m in GP services in 2016/2017 following contract negotiations, building on up to Â£5m committed in the previous year," she said.
"I also recently accepted the recommendations of the working group that was established to review GP-led care services here."
If members do vote by majority to leave later this month, the BMA will start collecting practice resignations.
This would mean that a patient who belongs to one of these GP practices will have to pay for their treatment, similar to the Republic of Ireland model.
In previous meetings in November and December, 97% of GPS signed to leave.
Northern Ireland's GPs will likely vote to leave the NHS if a snap election is called, says the chairman of the NI General Practitioners' Committee.