The federal government has lost its bid to have a challenge over prolonged Senate vacancies tossed out of court.

The government had appealed a Federal Court judge's refusal to dismiss the case outright.

But a three-member panel of Federal Court of Appeal judges has rejected that appeal.

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Aniz Alani, the Vancouver lawyer who is challenging the prime minister's right to leave Senate seats empty indefinitely, says the panel has also awarded him $1,500 in legal costs.

Alani launched the challenge last year when Stephen Harper was prime minister.

Harper stopped appointing senators in March 2013, amid the Senate expenses scandal; there were 22 vacancies in the 105-seat chamber by the time Harper's Conservatives lost power on Oct. 19.

"I'm pleased with today's unanimous decision of the Federal Court of Appeal, which is the second time our courts have rejected the government's claim that it's plain and obvious that a case concerning the prime minister's obligation to fill Senate vacancies has no chance of success," Alani said.

Liberal Prime Minister Justin Trudeau has created an arm's-length advisory board to recommend non-partisan nominees to fill Senate vacancies in a bid to return to the upper house to its intended role as an independent chamber of sober second thought.

The board, to which members were named just last week, is supposed to recommend potential appointees for five vacancies early this year and for the rest by the end of the year.

The appeal court judges last week questioned whether Alani's challenge is now moot, given that the new government is preparing to start appointing senators.

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Alani, who believes the court still needs to clarify whether the prime minister has absolute discretion to fill Senate vacancies when – or if – he chooses, says the appeal court panel ultimately decided Monday that the mootness issue should be decided by the lower court judge as part of the overall case.

Alani maintains that the prime minister has a constitutional obligation to fill Senate vacancies. He wants the court to declare that empty Senate seats should be filled within a reasonable time of falling vacant.

Federal lawyers have maintained it's the Governor General's constitutional responsibility to appoint senators; that it's only by convention that the appointments are made upon advice from the prime minister. They've argued that conventions are not enforceable by courts.