The federal government is putting its controversial First Nations education act "on hold" until the Assembly of First Nations "clarifies" its position on the legislation in the wake of the resignation of its national chief.

Shawn Atleo stepped down as national chief of the AFN on Friday, saying he was tired of being a lightning rod for criticism of the government's plan to overhaul the educational system on reserves.

Atleo supported the government's revised legislation, which was introduced by Prime Minister Stephen Harper in February, but faced opposition from regional chiefs across the country.

AFN regional chiefs from across the country gathered in Ottawa on Monday for an emergency executive meeting that aimed to choose an interim leader and set an election date for a new national chief.

But Aboriginal Affairs Minister Bernard Valcourt made his own surprise move, announcing that a second-reading vote on the bill would be put on hold in light of Atleo's resignation.

"Given the recent resignation of the national chief, following today's second-reading vote, any further consideration of this legislation will be put on hold until the AFN clarifies its position," Valcourt's office said in an emailed statement.

Roger Augustine, the Assembly of First Nations' regional chief for New Brunswick and Prince Edward Island and one of the few AFN chiefs who spoke to reporters on Monday, said he was surprised by Valcourt's move.

"Well, it's quite interesting now, because I don't think anyone really knows what's going to happen," he told reporters.

The government introduced draft legislation to change the way education is funded and controlled last fall. That draft bill was met with vocal criticism from First Nations leaders.

At a special assembly in December, chiefs listed five conditions they said the legislation must meet.

The revised legislation heralded by Harper in February was tabled in the House last month. Valcourt said it met the conditions set out by the chiefs and had the support of Atleo, but not all First Nations leaders were satisfied, leading to a movement to oust Atleo last week before he made his stunning announcement to leave on Friday.

"The First Nations control of First Nations education act provides the structures and supports necessary to help First Nations students reach their potential and become full participants in the Canadian economy. It would entrench in law the five conditions for success identified by the chiefs in assembly last December," Valcourt's office said.

'Pushing pause isn't enough,' says Liberal critic

But opponents of the bill say it gives too much control to the minister of aboriginal affairs, doesn't protect treaty rights, and the money attached falls far short of what is needed to make a difference for First Nations children.

"Pushing 'pause' isn’t enough. The government needs to listen to First Nations communities, who have been clear this bill is unacceptable in its present form," said Carolyn Bennett, the Liberals' aboriginal affairs critic.

"The government should take the time to sit down with First Nations and work with them to draft a bill that truly reflects First Nations control of First Nations education."

Valcourt said the government has undertaken unprecedented consultation leading up to the bill's creation, but critics said First Nations feel they were shut out of the process.

"It was once again an abject failure to consult adequately," said NDP Leader Tom Mulcair.

"When I saw a lot of the groups coming together last week — groups that don't often agree with each other — being unanimous that there had been no consultation, I knew that we were heading to a huge problem."

'Right thing for the time being'

One vocal opponent of the bill, Grand Chief Derek Nepinak of the Assembly of Manitoba Chiefs, said Valcourt should step aside and Harper should find someone who would properly consult and listen to the grassroots.

"They've got a couple of options they can play, but the right move right now was to pull it off the table," Nepinak said of the bill.

"They made a strategic decision and they've done the right thing for the time being."

Both Nepinak and Pam Palmater, chair in indigenous governance at Ryerson University, said the AFN executive must be cautious about taking any position on the bill at this time.

"If we come out of the gate now and we start trying to clarify our position on the bill, all we're doing is we're putting legitimacy into a process that I think has been flawed right from the start," Nepinak said.

Said Palmater, "They [the AFN] have to think carefully about how they respond to the minister. They can't come out and be making a decision about the bill because it's not their decision to make."