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Health Minister Ted Flemming says his department has asked Ottawa to extend the deadline for doctors to receive government subsidies. (CBC)

Doctors who have not yet enrolled in New Brunswick's new electronic medical record (EMR) system have missed a key deadline.

As of midnight on April 1, Canada Health Infoway, a federal agency, will no longer cover one-third of the $24,000 cost of the program.

Now doctors will have to cover more of the cost themselves, making the product a  harder sell.

About 950 doctors are eligible for the system, which is designed to digitize patient records in their offices.

As of late February, only 240 had signed up.

Last week, Health Minister Ted Flemming told the Legislature his department was talking to Ottawa about extending the deadline for matching money.

"I was advised those discussions were very close to coming to an understanding, some fruition, but they've not been completed," Flemming said.

By late Monday there was still no word of an extension, but New Brunswick Medical Society CEO Anthony Knight remained optimistic.

"We've expressed an interest to the department and we'd like to know as soon as we can if there is a change in the status of the funding from Canada Health Infoway," he said, ahead of the midnight deadline.

"But at the present time we're operating under today is the last day."

The Medical Society plans to release updated enrolment figures within a few days.

Knight says there was a surge of last-minute enrolments.

"Doctors are no different than any other individual in a community, and certainly we have seen a bump in the participation level from physicians," he said.

The New Brunswick Medical Society and the private IT firm Accreon set up a company called Velante to run the new software. Velante then contracted another company, New Zealand's Intrahealth, to build the system.

The cost of Velante's program — $8,000 per doctor even with the government subsidies — is one reason many refused to enrol. Other doctors questioned who will control patient data.

The original goal was to have 500 doctors signed up by Dec. 31, 2013.