Karolinska Institutet Innovations AB v. Attorney General of Canada, 2013 FC 715
The Applicant attempted to file a patent application with the Canadian Intellectual Property Office (CIPO) under the provisions of the Patent Co-Operation Treaty (PCT). The application was rejected by the Commissioner of Patents for a failure to submit the appropriate fees.
Although the lawyer and Patent agent having carriage of the matter had originally given specific instructions to her staff that the PCT Application was a "late entry" filing, the clerical logging system at the Patent agent's firm did not reflect that fact. Consequently, when the PCT Application was prepared for electronic filing with the Patent Office, the total fee amount set out on the electronic application transmittal documents was less than the full amount that was needed to cover the fee due at the time of filing.
CIPO did nothing until after the critical dates expired. It was not until about six weeks later that CIPO wrote a letter to the Canadian Patent agent, entitled "National Entry Refused". Upon discovery of the error, the agent attempted to pay the deficient fees. CIPO refused to accept additional fees and refused the national entry. The inventors applied for judicial review.
The Court held that the Commissioner’s decision was unreasonable and “lacked justification and transparency and was unintelligible.”  The Commissioner’s decision is set aside and the Commissioner is required to “issue a notice under Rule 3.1(2), requiring payment of the deficient fees.” 
Standard of Review
The Court held that reasonableness is the appropriate standard of review.
In this case the “Court is not being asked to consider what the Rule means; but rather, whether the Commissioner (CIPO) properly applied the Rule to the circumstances of the case. In this regard, the standard is reasonableness.” 
The Court held that that the Commissioner's decision “misapplied Rule 3.1 to the circumstances at hand.”  The issue that the Commissioner was required to address was “whether the Canadian firm filing the application had made, as stipulated by subsection 3(1) of the Patent Rules, a ‘…clear but unsuccessful attempt …’ to pay the required fee.”  The Commissioner's decision did not squarely address this issue.
“Rule 3.1 of the Patent Rules was introduced so as to provide the Commissioner of Patents a means, where there was a ‘clear but unsuccessful’ attempt to pay a fee, to attenuate the catastrophic effects that may otherwise happen. It does so by providing that the Commissioner can, within two months, send a notice under sub rule 3.1(2) that further fees are owing. Upon prompt payment of those fees, the application is deemed to be in good standing.” 
“Section 3.1 is a remedial provision; it is to be given a fair, large and liberal construction. A reference to ‘the fee’ can liberally be construed so as to include not only a basic filing fee, but also an additional filing fee for filing before the 42 month period.”