The Refugee Minister said there was "no possibility" of sending asylum seekers to Rwanda only eight days before the cruel scheme was unveiled.
Lord Harrington, who heads up the Ukrainian refugee scheme, was astonished by questions last week about the prospect of "offshoring" asylum seekers in the east African country.
Home Secretary Priti Patel is expected to sign the deal on a visit to Rwanda today, meaning desperate people seeking sanctuary in the UK would be flown 5,000 miles for processing.
In a speech in Kent later, Boris Johnson will boast he is “taking back control of illegal immigration” after Brexit.
But a senior Tory accused the Government of trying to create a "massive distraction" from the Prime Minister's Partygate fine.
Labour said the cruel scheme was "less about dealing with small boats and more about dealing with the Prime Minister's own sinking boat".
Last Tuesday, Lord Harrington told LBC: "We haven't sent any refugees to Rwanda."
Pressed on speculation plans were being drawn up, he said: "If it's happening in the Home Office on the same corridor that I'm in they haven't told me about it.
"I'm having difficulty enough getting them to Ukraine from our country.
"There's no possibility of sending them to Rwanda."
But Ms Patel touched down in Rwanda on Wednesday and is expected to ink the deal later today.
Mr Johnson will say action is needed to combat the "vile people smugglers" turning the ocean into a "watery graveyard".
He will add: “We cannot sustain a parallel illegal system. Our compassion may be infinite, but our capacity to help people is not.”
The Mirror understands senior Home Office officials have grave concerns over whether the scheme will provide value for money - or even act as a deterrent to asylum seekers arriving by small boats.
Ms Patel is said to have spent the last four months making the policy "just about viable" enough for the PM to be able to announce it.
Meanwhile the Nationality and Borders Bill that would allow asylum seekers to be sent offshore has still not passed - as rebellious peers say it will breach human rights.
Amnesty said the plan was "shockingly ill conceived" and warned that Rwanda had a "dismal human rights record".
Steve Valdez-Symonds, Amnesty International UK's Refugee and Migrant Rights Director, said: "Sending people to another country - let alone one with such a dismal human rights record - for asylum 'processing' is the very height of irresponsibility and shows how far removed from humanity and reality the Government now is on asylum issues.
"The Government is already wrecking our asylum system at huge cost to the taxpayer while causing terrible anxiety to the people stuck in the backlogs it has created."
"But this shockingly ill-conceived idea will go far further in inflicting suffering while wasting huge amounts of public money."
Welsh Secretary Simon Hart defended the plan as a "really humane step forward" but admitted that concerns had been raised about Rwanda's human rights record.
He told Sky News said: "It's an arrangement which I think suits both countries very well and provides the best opportunities for economic migrants, for those who have been in the forefront of this particular appalling problem for so long now.
"And I think that this arrangement is a really... it has the potential to be a really good step forward and a really humane step forward."
Pressed on the fact the president of Rwanda has been accused of human rights abuses on more than one occasion, Mr Hart said: "That is true, but that doesn't alter the fact that their reputation as far as migrants are concerned, and their economic progress, is phenomenal."
Senior Tory Tobias Ellwood slammed the move as an attempt to shift focus from Mr Johnson's Partygate law-breaking.
The chairman of the Commons Defence Committee said: "He's trying to make an announcement today on migration, and all of this is a massive distraction.
"It's not going away. It is a crisis. It requires crisis management. There needs to be a plan."
Labour's Lucy Powell told the BBC : "This is quite obviously a pretty desperate attempt by the Prime Minister to distract from his law-breaking and I don't think there would be many of your listeners that wouldn't take it with a large dose of scepticism.
"It's a plan that might sound good in a focus group and would certainly grab the headlines because it's very controversial and contestable - but in reality, it is unworkable, expensive, and unethical."
She added: "I think this is less about dealing with small boats and more about dealing with the Prime Minister's own sinking boat."
Mr Johnson will give a speech on the policy today despite it being the first day of purdah ahead of the local elections.
Ministers are advised not to announce long-term initiatives or use public money “for party political purposes” in the three weeks before polls open at 7am on Thursday 5 May.
