Therese Coffey said the government is preparing the next deportation flight to Rwanda after the first plane was grounded by legal interventions.
The pensions secretary said the government expected “a lot” of legal challenges but the home office was getting ready to try again.
Last night the European Court of Human Rights blocked the deportation and all the migrants were removed from the plane.
The court confirmed they had granted an urgent interim measure in regards to an Iraqi national, and it is understood they were considering a number of further requests.
Coffey told Sky News: “Frankly the government is disappointed in the decision. I’ve never known such a quick decision made by the ECHR...and I think the public will be surprised we have European judges overruling British judges.
“But nevertheless, I know the home office is already getting ready for the next flight.
“We will continue to prepare and try and overturn any future legal challenges as well.”
Asked how confident she was the next flight would be able to go ahead, she said: “I am highly confident.
“This decision was taken at rapid pace yesterday. As a consequence it is right that the government continues to try and make sure we deter unsafe, illegal routes of trying to enter the country because the only people who benefit are unscrupulous people traffickers, often trying to put people into modern slavery as well.”
Asked when the next flight will take place, she replied: “It’s for the home office to focus on their operational matters.
“I’m not sure it’s something I particularly want to broadcast. But nevertheless, preparations are underway and I’m confident that the home secretary Priti will be working with her team to take the next steps that are appropriate.”
Coffey declined to say whether it would be within days or weeks.
Home secretary Priti Patel said the ECHR intervention was “very surprising”, adding that “many of those removed from this flight will be placed on the next”.
She said the home office legal team is reviewing “every decision made on this flight”, and that preparation for the next flight “begins now”.
Rwandan government spokeswoman Yolande Makolo said: “We are not deterred by these developments. Rwanda remains fully committed to making this partnership work.”
Earlier, Boris Johnson suggested lawyers representing migrants were “abetting the work of criminal gangs” as last-ditch court hearings took place.
The prime minister had insisted the government would not be deterred from its policy, despite criticism from the Church of England and reportedly also from the Prince of Wales.
Yvette Cooper MP, Labour’s shadow home secretary, said: “There is no point in the government blaming anyone else but themselves. They have pushed ahead with a policy they knew was unworkable, unethical, and incredibly expensive because they just wanted a row and someone else to blame.
“They ignored all the warnings about the treatment of torture victims, the lack of proper processes in Rwanda, the fact that it will not stop criminal gangs, and the risk that it will make people trafficking worse. And they have still gone ahead with paying Rwanda over £120m.
“They are more interested in picking fights than in pursuing serious policies. This government has abandoned all British decency and common sense.”
Refugee Council chief executive Enver Solomon said they were “relieved” the flight to Rwanda did not take off as planned.
He added: “The fact that the final flight could not take off is indicative of the inhumanity of the plan and the government’s complete refusal to see the face behind the case.”