It has suggested it will review its tactics, conceding its response was not good enough and that it would not be allowed to happen again.
"
I would like to apologise to people who have had to put up with these atrocious conditions
"
David York, Highways Agency
Transport Secretary Alistair Darling responded to the chaos by demanding the road, rail and local authorities explain why they had not been prepared for freezing weather in the middle of winter.
The Highways Agency said heavy traffic prevented its teams from properly spreading grit on the M11 - one of the roads worst affected by the snow - on Thursday afternoon.
The agency, which is responsible for motorways and major roads, says gritting lorries were out from early afternoon.
But a spokesman said some motorists tried to leave early because of the snow, and the resulting traffic prevented the gritting teams from getting through.
Best practise guidelines
David York, the Highways Agency's operations director apologised to motorists caught up in the gridlock.
Speaking on the BBC's One o'Clock News, he said: "I would like to apologise to people who have had to put up with these atrocious conditions, stuck in vehicles for hours on end.
"
The gritting has been patchy at best
"
Graham Webb, AA Roadwatch
"That's just not good enough and I'm not prepared to let this sort of situation happen again.
"The advice at this stage is that our agents followed all of the processes that we put in place.
"Our best practice guidelines were followed."
He said 60 gritters were out in the "key links" of the M25, M11 and A14, from the middle of Thursday afternoon onwards.
But he conceded that if the process had not worked, they would have to review the situation to ensure no repeat performance.
Gritting costs
Graham Webb from AA Roadwatch admitted it was one of the worst days on the roads the organisation had ever seen.
He told the BBC: "The gritting has been patchy at best.
"There has been evidence of gritting particularly during the rush hour period, which is not particularly helpful."
Transport Secretary Alistair Darling has demanded an explanation.
He said: "Snowfall in January is hardly unexpected.
"I have asked the Highways Agency, the rail industry, tube and local authorities for an explanation as to why the transport system in some parts of the country became paralysed so quickly."
It is not the first time the Highways Agency has faced criticism for the way it deals with snow.
In 1995 the M25 in Surrey and Kent ground to a halt because they weren't gritted.
Again, the Highways Agency then blamed heavy congestion.
The AA says too often cost cutting is resulting in roads not being cleared of snow quickly enough.
It says a salting run can cost about £30,000, so lots of money can be saved by cutting back.
The AA wants legislation to require local authorities in England and Wales to make gritting roads a priority.
The legislation already exists in Scotland.