The first flight taking asylum seekers to Rwanda will take off and people who are not removed on Tuesday will be on subsequent flights, Liz Truss has said.
The foreign secretary said it would "establish the principle" and break people traffickers' business models.
Seven or eight people are due to be removed on Tuesday, after dozens won legal cases to be taken off. But more legal challenges are set to be heard.
Church of England leaders described the plan as an "immoral policy".
Prime Minister Boris Johnson has said the government will not be "deterred or abashed" by criticism of the plan.
Four more legal challenges from people set to be flown to the east African nation's capital Kigali are expected to be heard in the courts before the flight departs, after a last-ditch attempt to block the flight altogether was rejected by the Court of Appeal on Monday.
On Monday 138 people reached the UK in three boats, with more than 10,000 migrants making the dangerous journey so far this year.
Speaking to BBC Breakfast, Ms Truss confirmed the flight will depart as scheduled even if only a small number of people were on board, describing it as a "key part of our strategy for tacking the appalling people smugglers who are trading in people's hopes and dreams".
She said: "If people aren't on the flight today, they will be on subsequent flights to Rwanda."
Ms Truss added the government was prepared to "face down" future legal challenges to its plans, adding: "It's about making sure that people have a safe future in Rwanda and we're determined to follow through on it".
Asked on BBC Radio 4's Today programme if the plane would take off even if no one was on board, Ms Truss said she was confident there will people on the flight - but added she was not able to say how many it would be.
However, she said the numbers of people being sent to Rwanda by the end of the year "will be significant".
She also declined to say how much the flight would cost, but argued the cost of human trafficking and illegal immigration was "huge" to the taxpayer.
The flight on Tuesday evening was originally due to carry dozens of passengers, but most succeeded in their individual appeals against removal.
It is not clear exactly how many will leave on the flight: on Monday night, the Home Office said it was eight, while the charity Care4Calais said the number had fallen to seven.
In a letter to the Times, senior Church of England leaders described the plan as an "immoral policy that shames Britain".
Signed by the archbishops of Canterbury and York and more than 20 other bishops who sit in the House of Lords, the letter said that "those to be deported to Rwanda have had no chance to appeal, or reunite with family in Britain".
"They have had no consideration of their asylum claim, recognition of their medical or other needs, or any attempt to understand their predicament."
Speaking in cabinet on Tuesday, Mr Johnson said the government were "going to get on and deliver" on its plan, despite the "criticism that is being directed upon this policy, some of it from slightly unexpected quarters".
He told ministers the objective is to ensure there is a "clear distinction" between immigration to the UK by safe and legal routes that the government supports and "dangerous and illegal cross-Channel migration, which we intend to stop".
Tuesday's flight is due to be the first in a five-year trial, in which some asylum seekers deemed to have entered the UK illegally are transported to Rwanda to claim refuge there.
They will get accommodation and support while the Rwandan government considers their application, and if they are successful they can stay in the country with up to five years' access to education and support.
If their asylum claim is unsuccessful, they will be offered the chance to apply for other immigration routes, but could face deportation from Rwanda.
The letter to The Times, signed by the entire senior leadership of the Church of England, said those being sent to Rwanda have had no chance to reunite with family in Britain.
"Many are desperate people fleeing unspeakable horrors. These are people Jesus had in mind as he said when we offer hospitality to a stranger, we do it for him," it says.
"We cannot offer asylum to everyone, but we must not outsource our ethical responsibilities, or discard international law - which protects the right to claim asylum."
It's not the first time the Archbishop of Canterbury has criticised the plan - he described it as "the opposite of the nature of God" in his Easter sermon.
At the time, the Home Office responded that the UK had a "proud history" of supporting those in need.
The BBC has contacted the Home Office for a response to the letter.
At-a-glance: The Rwanda policy so far
- The PM announces the five-year £120m trial in which some asylum seekers will get a one-way ticket to Rwanda
- It faces widespread opposition from more than 160 charities and campaign groups, a small number of which launch a legal challenge
- Home Office lawyers say the plan is in the public interest - and the High Court agrees
- Campaigners appeal against the ruling but are unsuccessful
- Judges will consider whether the policy is lawful next month - this could see some people returned to the UK from Rwanda if it is ruled unlawful
On Monday, appeal court judges ruled the first deportation flight could go ahead, agreeing with a previous judgement that it was in the "public interest" for the government to carry out its policies.
Campaigners had hoped to stop the plane taking off before a full court hearing on whether the policy is lawful next month.
Speaking in the Commons on Monday, Labour's shadow home secretary Yvette Cooper described the plan as "profoundly un-British".
But Rwanda's high commissioner Johnston Busingye earlier defended the partnership, telling the Daily Telegraph people arriving in the country would be treated with "safety, dignity and respect".