It is appealing a ruling last month by Federal Court Justice Sean Harrington, who rejected a government motion to dismiss the case.
The case was launched by Vancouver lawyer Aniz Alani, who is asking the court to declare that Senate vacancies must be filled within a reasonable time.
Harper has not appointed a senator since March 2013 — when the scandal over senators' allegedly improper expenses began to engulf his government.
There are currently 20 vacancies in the 105-seat, unelected upper house.
Alani contends the prolonged vacancies are unconstitutional, leaving provinces under-represented and the Senate less able to carry out its constitutional duty as the chamber of sober second thought.
The government's notice of appeal comes just as it's bracing for more bad news about allegedly improper expense claims. The results of a comprehensive review of senators' expenses by auditor general Michael Ferguson are to be handed over to the Senate this week.
The trial of disgraced Sen. Mike Duffy on bribery, fraud and breach of trust charges resumed Monday as well.
In its notice of appeal, the government says Harrington erred in allowing Alani's application for judicial review of Senate vacancies to proceed. The government maintains it's "plain and obvious" that the matter is not justiciable, is outside the jurisdiction of the Federal Court and has no chance of success.
Harrington has not yet heard arguments or ruled on the substance of Alani's challenge. But in rejecting the government's bid for dismissal last month, he suggested there is an obligation to appoint senators, no matter how distasteful in the midst of scandal.
"From time to time the Senate, or some senators, may be a source of embarrassment to the government, to the House of Commons as a whole and, indeed, to many Canadians," he wrote.
"However, I know of no law which provides that one may not do what one is otherwise obliged to do simply because it would be embarrassing."
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