Premier David Alward visited the northwestern village of Perth-Andover to survey the damage first-hand, which was estimated at around $25 million.
Some 500 residents were ordered to leave for higher ground Friday after the river spilled its banks.
"It was something beyond imagination," Alward told a news conference.
Alward said there was significant damage to government buildings and about 150 properties in the community, which declared a local state of emergency on Friday. It was still unclear when evacuees would be able to return home.
"I know the last few days have been an unbelievably difficult time for this community," he said.
"I sympathize with those folks who have been forced out of their homes by the rising flood waters, the families whose lives have been thrown into chaos the last few days, and the small business owners who are watching their livelihoods become devastated by this event."
Flood waters had receded Sunday on the village's main street, leaving behind a mess of mud and truck-sized chunks of ice.
The village of 1,700 has endured four major floods since the 1980s, the most recent in 2008. Water levels this time around reached at least a metre higher than in any previous flood, said officials.
Hector Guitard, who owns a hardware store in the village, said while his basement has flooded in the past, he's never seen anything like this flood.
"I had about six feet of water on the main floor, so stuff fell over and it's now laying in mud," he said. "Hopefully we can get back in there as soon as possible and get it cleaned up."
The local hospital remained closed because it was flooded.
Alward reassured residents Sunday that the hospital will reopen, though he could not say when.
"People can have full assurance in the importance of the hospital here," he said.
Unseasonably hot weather that caused a rapid snowmelt and an ice jam was being blamed for causing the St. John River to breach its banks.
The flooding also damaged a few homes on the nearby Tobique First Nation and forced some 50 people to leave the reserve over the weekend.
Public Safety Minister Robert Trevors said residents will be able to begin the process of filing an assistance claim on Monday.
A toll-free hotline (1-888-298-8555) has been set up for people to call.
"The program will allow residents to receive information and register their flood-related damage with a single phone call," said Trevors.
The province's Emergency Measures Organization said people could be eligible for up to $100,000 in assistance under the federal-provincial relief plan.
Inspectors will assess what repairs are needed before people can safely return to their properties. The government said people whose claims are approved could be eligible for an advance payment up to $4,000 for immediate repairs.
Trevors said inspectors have already begun assessing properties in Perth-Andover and on the Tobique First Nation.
Perth-Andover Mayor Rick Beaulieu said he understands people want to get back into their homes as soon as possible, but urged patience.
"We want to make sure that when they go back into their homes or their businesses that everything is safe," he said.
"That's why it's important that these inspection teams have a chance to view these properties and make sure there are no hazardous situations."
A similar relief program was offered in December 2010 after days of rain caused rivers to breach their banks, flooding homes and businesses in St. Stephen.