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More than 700 staff will be recruited as leadership of reducing the number of asylum seekers reaching UK shores – such as the Kent coastline – returns to the Home Office.
The newly-created Small Boats Operational Command (SBOC) will introduce new air and maritime capabilities including new drones, boats, land-based radar and cameras.
It comes after the military were brought in last year to tackle small boats in the Channel.
But from today, SBOC – which is part of the Border Force – brings together the government’s response to small boats under a single structure.
The Home Office says 730 additional staff will be recruited, with 100 of these located inside its UK headquarters, while "the remainder will bolster operations".
And there will also be new air and maritime capabilities introduced under SBOC, including new drones, boats, land-based radar and cameras.
It is hoped it will help track vessels on the water, identify pilots and help to bring those responsible to justice.
A government spokesman said: "Last year we saw an unsustainable and unacceptable number of people risking their lives to reach the UK illegally.
"This simply cannot continue and that is why we are taking immediate steps to tackle the evil people-smuggling gangs behind these deadly crossings and get our immigration system under control.
"The return of Channel primacy to the Home Office, bolstered by 730 extra staff and led by director Duncan Capps, is a significant landmark in our long-term plan to ensure the safety and sovereignty of our borders and our communities.
"We are building on the progress already made through the new deal with France, and our determination will not waiver until we stop the abuse of the asylum system and bring the smugglers responsible to justice."
The Home Office says military leadership of the operational response to Channel crossings was "always intended to be a temporary measure" and scheduled to end this month.
However, it says SBOC will continue to work closely with the military in a handover period to respond to Channel crossings.
Plain-clothed military patrols were spotted on the Kent coast last week in a bid to tackle small boat crossings.
High-speed rigid inflatable vessels belonging to military units are reportedly operating in the Channel close to the shoreline to look for vessels which have made it past other Border Force and Royal Navy patrols.
Boats were seen operating out of Dover Harbour on Wednesday and it is understood the plain-clothed military personnel are working as part of a joint-effort by the government to tackle the high number of crossings being made.
Dover MP Natalie Elphicke paid tribute to the work undertaken by the military and urged vigilance in observing and reporting small boats landings.
She said: “Whenever the military come to Dover and Deal, be that to sort out aftermath of the French border closure, stand up community Covid testing or bring order to the border on Channel Command operations, they do a brilliant job. "Their professionalism and expert skills have resulted in significant changes in detection and interception,
“It is vital that this is maintained as the Home Office take back control of the Channel Command.
"It’s important to make sure that all beach landings are reported. Please don’t leave it to someone else.
“While these small boats crossings continue they put a huge strain on local services.
"With numbers of arrivals forecast to rise even further this year, a successful outcome from the March Summit between the Prime Minister, Rishi Sunak, and President Macron is crucial.”