A Canadian soldier has lost a legal battle to recover tens of thousands of dollars he lost when posted to a new city, even as the judge hearing the case questions the fairness of the government policy denying him more compensation.

"I am disappointed with the decision," Maj. Marcus Brauer wrote on a GoFundMe page set up to raise money for his court case.

In 2010, Brauer lost $88,000 in equity when he was forced to sell his home in Bon Accord, Alta., to move to Halifax for a new posting. He was only awarded $15,000 worth of compensation.

Brauer took the federal government to court. He argued he should be reimbursed the entire $88,000 under a federal home equity assistance program that's supposed to cushion the financial blow when military members are forced to sell in so-called depressed housing markets.

Brauer lost $88,000 in equity on the sale of this home after he moved from Bon Accord, Alta., to Halifax. (CBC)

In a ruling this week, Federal Court Justice Robert Barnes dismissed Brauer's case, and said he was treated fairly under the current government relocation policy.

"It is not the role of this Court to rewrite the government relocation policy for CF members which, without doubt, imposes most of the financial risk of home equity losses on CF members who are required to relocate," wrote Barnes.

Brauer said on the GoFundMe site that this is the end of his legal battle. Brauer also said he learned a great deal about the damage financial stress can have on a family.

"I wanted to advise my supporters that the government has worn us out despite my best efforts," wrote Bauer. "I wish I could have done more, just as much as I wish my superiors would have done more to provide support over the years. We have to accept this decision and try to move on."

'A valid political concern'

The ruling comes as separate case, a proposed class action, is making its way through the courts. It claims other Canadian Forces members have been unfairly denied compensation after suffering steep losses on home sales after being posted to new locations by the military.

Military members can receive 100 per cent compensation for significant home sale losses under the home equity assistance program only if they sell in what's considered a depressed market.

To get that money Brauer had to show housing prices in Bon Accord had decreased by 20 per cent from the time he bought his house to the time he sold it.

Brauer argued Bon Accord met that requirement while the Treasury Board, which controls compensation, refused to pay.

That led to a court battle between Brauer and the federal government. In 2014, a Federal Court judge ruled the Treasury Board was unreasonable in denying Brauer further compensation.

The federal government was even ordered to pay Brauer's legal costs and the case was sent back to be considered a second time. However, the Treasury Board once again rejected Brauer's claims for compensation and the case went back to court last year.

This latest ruling dismissed Brauer's case and sides with the government. However, Barnes did have concerns about the government's relocation policy.

"The fairness of government policy is a valid political concern but it is not, on its own, a basis for judicial relief," Barnes wrote.