The payment issue became public after a lawyer indicated Friday he was stepping aside because he hadn't been paid.
Douglas Elliott was granted full standing to represent the Elliot Lake Mall Action Committee and the Seniors' Action Group of Elliot Lake at the inquiry.
But Elliot told the commission Friday that he is suspending involvement after consulting his clients because funding that the government promised has yet to come through.
A spokeswoman for Ontario's Attorney General sent an email on Saturday that indicates the government has processed outstanding bills and payments should be received soon.
Two people died in last summer's collapse of the Algo Centre Mall.
The inquiry began last month and is expected to run through the summer and hear from 75 witnesses.
Elliott blasted the government on Friday for not paying quickly, saying it does a disservice to Elliot Lake residents.
"I think this is extremely disrespectful of the commission," the lawyer said Friday, according to a draft transcript.
"I think it is disrespectful of the people of Elliot Lake. The people of Elliot Lake have learned through this inquiry that there have been people who have put money ahead of the interests of the people of Elliot Lake, and regrettably, it appears that the government of Ontario is doing that now."
The commission makes recommendations to the Ministry of the Attorney General, which has final say on who gets funding and pays those involved.
Elliott is part of a team representing ELMAC, which speaks for those injured in the collapse along with store owners and mall employees, and community group SAGE.
Both were both granted full standing and given funding for two lawyers by the commission in November. Earlier this month the groups filed a joint request for money to take on another two lawyers, citing a heavier workload than expected.
The City of Elliot Lake also filed an April motion calling for more money that would let it increase its daily legal workload by taking on two more lawyers — up from the current two counsel and law student working for the municipality at the inquiry.
The families of Lucie Aylwin, 37, and Doloris Perizzolo, 74, who died in the June, 2012 collapse, are being represented by separate lawyers and have also been given full standing.
In an open letter to Premier Kathleen Wynne, New Democrat MPP Michael Mantha also hammered the government's failure to pay some of the inquiry's bills, saying it's jeopardizing the commission's ability to seek answers in the mall collapse.
"One would think that after everything this community has been through, the least the government can do is pay its bills on time, so there’s no delay in this important inquiry," Mantha said in a news release issued Saturday.
Also on HuffPost