The government tried to launch an income tax audit of the rideshare company last February.
But over the ensuing six months, Uber provided no response or only partial responses to 16 of 29 requests to see the company's books, the CRA claims in a Federal Court filing.
Uber says this was a routine audit and that it has fully cooperated with the authorities.
The government says it gave Uber several deadline extensions. Finally, in October of last year the CRA went to court to force Uber to open up its books.
"The Minister sought and continues to seek the respondent's books, records and documents in order to determine whether (Uber) has complied with its duties and obligations under the Income Tax Act and properly computed and reported taxable income," reads the filing.
The government says Uber offered "various explanations" for not granting access to its books.
Uber says that the CRA's deadline actually fell on October 16, the same day the government's court action was filed. Uber says it is cooperating with the audit and made its response on that date.
The CRA dropped its legal action 11 days after filing it.