In a note on its website Wednesday morning, the tax agency provided little detail.
"To protect the security of taxpayer information, we have temporarily shutdown public access to our electronic services. We are working to restore these services as soon as possible in a manner that ensures they are safe and secure," the website read.
In a message posted on its website in early March, the agency, still commonly known as Revenue Canada, warned Canadians are being targeted by fraudulent emails and phone calls from people posing as agency officials.
It's uncertain if the website's partial shutdown and the email and phone scam are related.
The agency tweeted days earlier that 1,763 online returns were being processed per minute.
More than 6.7 million Canadians have filed tax returns electronically as of March 24. That represents almost 84 per cent of returns.
The 2014 deadline for personal income tax filing for the 2013 tax year is end of this month.