Several groups that had considered applying backed out because they believe the state's proposed regulations are too restrictive for the businesses to work.
They also say it's not fair for them to apply to the state, put up the $20,000 fee and possibly publicly expose details of their plans when the regulations could still be in flux.
The confusion and wrangling means that a little over a year after the state became the 14th in the nation to legalize medical marijuana, patients who would qualify don't have legal access. Patients and some medical experts say the drug can ease pain and nausea for patients with conditions including glaucoma and multiple sclerosis.
The state's proposed rules, which have been delayed and revised over the past year, have not been finalized.
The state Legislature has already declared that the rules drafted by Gov. Chris Christie's administration do not follow the legislature's intent. Through a rare constitutional action, lawmakers could void them. No vote to do so has been scheduled - and none can be until next week.
One organization made up of about 30 prospective alternative treatment center owners filed legal action to try to delay the deadline. The Association of Safe Access Providers was hoping for a state court to rule sometime Monday afternoon.
"The goal is to get that pushed back until the state follows the law," said Justin Alpert, a lawyer for the group.
Alpert said most would-be marijuana providers he knows have decided not to apply because of the confusion over what rules might be implemented, and the state of the current draft regulations.
Chris Goldstein, the spokesman for the Coalition for Medical Marijuana of New Jersey, said he's aware of only four groups who have decided to move ahead with their applications.
McKinley Brown and two partners want to open an alternative treatment center in Newark, but say they're not applying. Their organization, CFM Jr., is a plaintiff in the effort to get Monday's deadline delayed.
Brown said his main objection to the proposed rules is a rule that none of the 13 other states with legal medical marijuana has imposed: Capping the amount of THC, the main psychotropic substance in marijuana, at 10 percent.
"You invest $300,000, $400,000 into equipment," he said. "Your cap grows and it's over 10 percent, they take it."
He said it could take up to four years to grow a crop that meets the state's proposed requirement.