Soldiers and riot police are manning the entrance of the building.
It follows last week's court ruling that NFF president Amaju Pinnick lost his post to Chris Giwa in elections in September 2014.
Giwa and his team had said they would occupy and take over the NFF offices to start work on Monday.
The NFF has appealed against the court ruling, insisting that Pinnick is still the head of the federation.
And staff of the Fifa-recognised NFF, including the general secretary Mohammed Sanusi, are currently working in the building.
Giwa's faction and all other non-NFF staff have been denied access into the football house by police, who have been in attendance since Sunday.
"We got here this morning and the police requested our identity cards, then we were let into our offices," an NFF staff member told BBC Sport.
"Only those without any proof of NFF identifications are prevented from coming to the building."
The ongoing power struggle means Nigeria face the prospect of a Fifa ban, which could put their World Cup qualification hopes in jeopardy.

The adult comedy, starring Mila Kunis and Kristen Bell, took £1.47m in its first week, falling just behind the animated Pixar film.
Finding Dory took another £1.51m, bringing its total UK takings so far to £35.8m.
Suicide Squad dropped one place to third, with takings of £1.27m, followed by new entry War Dogs.
The comedy drama, starring Jonah Hill and Miles Teller, is based on the true story of two men in their 20s who won a contract to arm America's allies in Afghanistan.
The top 10 also saw a new entry for horror film The Purge: Election Year, which took £807,803 in its first week.
Mechanic: Resurrection, a thriller starring Jason Statham, debuted at number 10, with a total of £508,715.
Jason Bourne is in the charts for a sixth week, taking £732,632 and the number six spot this week, with The BFG following in seventh place with £658,840.
Lights Out - another horror film - took £558,167 in its second week of release and is in eighth place, with David Brent: Life on the Road at number nine with £508,762.
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Eight of the accused, all senior managers, are charged with murder over the Soma coalmine tragedy in western Turkey last year.
The trial was adjourned until Wednesday because the court said the accused must testify in person, not via video link.
An underground fire sent deadly carbon monoxide through the mine. An inquiry criticised the mine's safety measures.
It was modern Turkey's worst industrial accident.
The trial at Akhisar, about 50km (30 miles) from Soma, drew several hundred angry relatives to the special tribunal, but police prevented them from getting in.
The BBC's Turkey correspondent Mark Lowen says the government is shielding state officials from any investigation, despite claims that they were aware of safety deficiencies at the mine but failed to act.
The managers facing murder charges could be given up to 25 years in prison.
Protests broke out after last year's disaster, fuelled by an apparently insensitive comment by President Recep Tayyip Erdogan, who was prime minister at the time. He said accidents were "in the nature of the business".
The International Labour Organisation says Turkey has the third-highest rate of workplace accidents in the world.
Security forces are controlling who enters the main office of the crisis-hit Nigerian Football Federation in the capital Abjua, BBC Sport has learned.
[NEXT_CONCEPT]
Finding Dory has clung on to the top spot in the UK box office - despite the threat from nearest rival Bad Moms.
[NEXT_CONCEPT]
Turkey has begun the trial of 45 managers and employees charged over a mine disaster which killed 301 people.