The facility is still open and will continue to be used as needed to carry out initial checks on arriving migrants.
At its peak earlier this month, 4,000 people were being housed at the site — at least double its 1,600-person capacity — in what was branded as a “breach of humane conditions”.
Since then, numbers have gradually declined as people were moved out of the site.
“Manston, by design, is meant to be a temporary holding facility, where people are processed before moving on — normally, fairly quickly,” said the prime minister’s official spokesman.
“Obviously there were immediate challenges, particularly after the attack at the other centre, which caused numbers to spike, so you would expect numbers to be relatively low on a daily basis as people are moved through quickly.”
In December, an attacker carried out a petrol bombing on a British immigration border force facility in Dover.
Migrants at immigration processing centre in Manston — in pictures
More than 42,000 migrants have arrived in the UK so far this year after crossing the Channel, provisional government figures show.
No journeys have been recorded by the Ministry of Defence for the past seven days amid bad weather.
It comes as a man died in hospital after being held at the processing centre.
It is thought he crossed the Channel on November 12 before being taken to Manston.
Immigration minister Robert Jenrick said there was no evidence at this stage to suggest the death was caused by an infectious disease and it is suspected the man was already unwell before he came to the UK.
A postmortem is due to be carried out and the case has been referred to the Prison and Probation Ombudsman and the Independent Office for Police Conduct.
But the police watchdog said it had reviewed the case and will not be investigating as it “does not have the jurisdiction” to do so and the matter does “not fall under our remit”.
Migrant crossings on the English Channel surge amid heatwave — in pictures
The former military airfield near Ramsgate has been dogged by controversy over the past few weeks, with ministers coming under fire over conditions.
Last month, chief inspector of borders and immigration David Neal told MPs he was left “speechless” by the “wretched” conditions at the site and laid bare the scale of the overcrowding chaos when he warned Manston was already past the point of being unsafe.
The facility is designed to hold migrants for a maximum of 24 hours but stays of up to five days are permitted in exceptional circumstances.
Does the UK have a migrant crisis? — video
But Mr Neal described how he had met families who had been living there for a month and had to sleep on the floor of a marquee.
A week later, chief inspector of prisons Charlie Taylor called on the Home Office to “get a grip” on the problems at the site and said the government department and its contractors must “speed up the processing of migrants so people can be moved off the site as quickly as possible”.