Prime Minister Rishi Sunak has labelled the small boats crisis a priority for his premiership.
The 90 people who arrived on Sunday were taken to Western Jet Foil processing centre in Dover, the ministry confirmed.
A government spokesperson said: “Nobody should put their lives at risk by taking dangerous and illegal journeys.
“We will go further to tackle the gangs driving this, using every tool at our disposal to deter illegal migration and disrupt the business model of people smugglers.”
Earlier this month, Mr Sunak announced a range of measures to tackle the issue including 700 staff for a new unit to monitor small boats crossing the Channel.
He also promised more staff to help clear some of the UK’s backlog of asylum cases by the end of next year.