Officials said a series of operations took place across the country over the past few days, with more activity due to be carried out in the coming weeks.
It comes amid the Government's bid to get flights off the ground by July, after the Safety of Rwanda (Asylum and Immigration) Act became law last week.
The Home Office confirmed it has now begun detaining failed asylum seekers.
Migrants in in handcuffs were escorted to vans after raids on homes and hotels across the country.
The first group were detained on Monday, the Daily Express understands.
The Home Office has refused to say how many people have been held. But women were among those detained in the first 48 hours, it is understood.
Protesters have targeted the visits, with tactics that apparently include lying in front of Home Office immigration enforcement vans to prevent them leaving.
Home Secretary James Cleverly said: "Our Rwanda partnership is a pioneering response to the global challenge of illegal migration, and we have worked tirelessly to introduce new, robust legislation to deliver it.
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