Delivering his decision after a one-day hearing, British judge Jonathan Swift said it was in the "public interest" for Interior Minister Priti Patel "to be able to implement immigration control decisions."
That includes London's plan to rid Britain of migrants and asylum seekers by sending them one-way to Rwanda.
The UK government intends to fly the first planeload of claimants to Rwanda on June 14, after agreeing the plan with Kigali in a bid to deter illegal migrants from undertaking perilous crossings of the Channel by boat.
Refugee rights groups and a trade union representing UK Border Force personnel challenged the plan in London's High Court, seeking an injunction against Tuesday's inaugural flight and any beyond then.
They argue that the plan violates asylum seekers' human rights, and say the government cannot justify its claim that Rwanda is a safe destination.
Home Secretary Patel asserts otherwise. "Rwanda is a safe country and has previously been recognized for providing a safe haven for refugees," she stated.
But rights groups bidding to block the policy said they were "disappointed", while one faith leader said it left her feeling "deeply ashamed to be British"
"It feels inhumane," the Bishop of Dover Rose Hudson-Wilkin told Times Radio of the planned deportations.
Enver Soloman, chief executive of the Refugee Council, said it was "extremely worrying that despite these legal challenges and widespread concern, the government remain determined to press ahead".
The UN agency's lawyer Laura Dubinsky said it "in no way endorses the UK-Rwandan arrangement".
Dubinsky said the would-be refugees were at risk of "serious, irreparable harm" if sent to Rwanda, and that the UN had "serious concerns about Rwandan capacity".
The UNHCR's concerns include a lack of legal redress in Rwanda and potential discrimination against gay claimants.
In issuing his ruling, Judge Swift gave permission for it to be appealed, suggesting Court of Appeal judges would hear the case on Monday, while also setting the date for a fuller two-day High Court hearing next month.