A spokesman for Northamptonshire Fire and Rescue Service said that several appliances were still on site after the discovery of a number of 'hot spots'.
Firefighters worked through the night to ensure that the blaze did not spread to other nearby factories and warehouses.
Speaking last night, Martyn Emberson, chief fire officer for the county's fire service, said: "The fire is under control but at we are fighting it defensively to make sure it does not spread."
The blaze, which could be seen from several miles away, broke out just after 2pm at Garrard Waters, a flooring company based in Caswell Road.
Mr Emberson added: "We have three ladder aerial platforms which are putting water down on the fire from above. It's extremely dangerous inside. There is a lot of carbon monoxide and carbon dioxide as well as other chemicals from all the burning plastic from the carpets inside.
"The water we are using is from the three ponds by Brackmills using a high volume pump, but that took a long time to set up. We are also using the Corby unit to supply water."
Speaking earlier from the scene, supervisor Robert Stevenson, said: "There's about 40 people working here and we go them all out within a minute so everyone is accounted for. The whole place has gone up."
Mr Stevenson said the warehouse was 60,000 sq ft in size and at least six fire crews were fighting to keep the blaze from spreading to neighbouring premises, including a chemical firm.
Garrard Waters, which is part of the Headland group of companies, has been based in Northampton for more than 50 years and has been in Brackmills for the past 18 years. It supplies carpets and vinyl flooring to the retail sector.
Nobody is believed to have suffered any ill-effects from the fire, but police warned that thick, acrid smoke was billowing across the nearby A45 dual-carriageway and they were urging people to keep their windows closed.
Roads surrounding the area were closed off and hundreds of workers sent home early as a result of the blaze.
John Gillett, a car valeter who works at car auction company Manheim in Brackmills, said he first noticed the blaze when smoke started pouring out of the building.
He said: "Smoke just started coming out and it hasn't gone down. There are 50ft flames coming out, and they aren't getting any smaller. There's a rumour going round that if the wind changes we will have to evacuate - we wouldn't be able to breathe.
"Someone said 'look that that' and we all just saw the flames getting bigger and bigger.
"It looks like a bomb has gone off or something. I've never seen anything like this."
See Wednesday's Chronicle & Echo for exclusive coverage of the fire