General Sir Gordon Messenger said he did not yet know how many of the 23 million people going into Tier 3 will be able to access the regime, as "planning is still very much under way".
But he told a Downing Street press conference that capabilities will "sequence over time", adding this will be into "January and beyond".
It comes after Boris Johnson signalled last week that mass community testing was the way out of Tier 3 restrictions, referring to the "success story" of Liverpool, where the scheme was piloted.
In response to a question on how many people in the toughest tier will be able to access mass community testing, Sir Gordon said he did not yet know how many it will reach.
"And as I said, the nature of this will vary from region to region and from area to area," he said on Monday evening.
"We are alive to the possibility that we will not be able to do this all at once, but we assess that local authorities are at varying levels of preparedness and readiness to do this.
"And therefore I can see this as an offer that will sequence over time and into January and beyond.
"The priority that we accord, the levels of support we give, will be based on the infection rate, how long those areas have been under harsh restrictions, how mature their plans are, how ready they are to deliver them."
He added that the next week would be identifying the "front runners" in the ability for community testing and to "lean in" to support them.
Meanwhile, the Department of Health and Social Care (DHSC) announced that local authorities in Tier 3 areas will be able to apply for a six-week community testing programme in a bid to drive down transmission.
The Government said it will work with local authorities to develop initiatives to encourage people to take part in order to detect as many cases as possible.
Health Secretary Matt Hancock has previously said that the testing regime in Liverpool, which was supported by about 2,000 troops, helped the area move from Tier 3 before the lockdown to Tier 2.
But Sir Gordon told the press conference that while the programme in Liverpool was led by a primarily military workforce, this would be "simply undeliverable" for all of the country.
"I can say with confidence that cannot be replicated around the country, and therefore the military support, along with all other types of central support, has to be targeted where it's needed most and where it can have the greatest effect," he said.
"I have absolutely no doubt that the military will continue to play a really important part in the community testing programme but the baseline assumption in terms of workforce generation is that that will be delivered locally with considerable support from the centre.
"So that is our starting assumption, as I say, I've no doubt that the military will play a prominent role, but the idea that it can be a wholesale offer to all local authorities is simply undeliverable given what the military are doing already."
He also urged moving away from the term "mass testing", adding: "I think this is about community testing.
"It's about tailoring to the needs, as I said, of the local area, and that might be geographically specific, or it might be ethnic community specific."