The Canada Revenue Agency says it now knows what caused the problems that led it to shut down its computer system for income tax filing, but warns it will still be days before it's fixed.

"Today is better than yesterday," CRA commissioner Michel Dorais told CBC News Wednesday. "We worked throughout the night and I'm pleased to say today that we've diagnosed the problem exactly."

Dorais said the problem began shortly after 20 maintenance operations were carried out on the weekend. On Monday, the tax department noticed "some irregularities" in its databases and quickly shut down all online access to Efile, Netfile and My Account. Dorais called it an infrastructure problem and said the data is completely secure.

"The databases are intact," he said. "It's not a virus. It's not an intrusion."

Dorais said the fix is a major one, involving 75 separate databases that handle individual returns. He said the databases are being gradually brought online but warned that the fix won't be immediate.

"We're hoping to solve the problem and to fix it fairly quickly," he said. But the databases that allow the e-filing of returns are "the biggest and most complex … so will be the last to come online."

Dorais said daily updates will be posted on the Canada Revenue Agency web site.    

When asked if the temporary shutdown will prompt the CRA to extend the normal April 30 tax filing deadline, Dorais said, "We're not there yet."  

About 1.4 million Canadians had already filed returns by the end of February, with about half of those filing online. Business returns are not directly affected, the agency said.