The bonfire, which has been built just yards from the buildings, is one of many set to be ignited in loyalist communities across Northern Ireland over the weekend.
The fires are an "Eleventh Night" tradition ahead of the "Twelfth of July" high-point of the loyal order marching season.
A bonfire has been lit on the site for many years, but this summer it is much larger than before - prompting the Fire Service to warn nearby residents of the dangers.
It is understood the structure has been built bigger this July because a play park is being constructed on the site in the coming months, so this bonfire is set to be the last.
The bonfire sits on grassland on a section of the popular Comber Greenway cycle path.
The land is owned by Stormont's Department of Regional Development. The department co-ordinated today's work to board up the at-threat properties.
Alliance party Assembly Member Chris Lyttle said the bonfire was "dangerously close" to residential and community properties.
"We are working with people to help them celebrate culture and tradition in a positive manner, but the size and location of this particular bonfire now poses a serious risk to residents, a community centre and a dedicated cycle and walkway," he said.
"It is unacceptable in 2015 that a government department has allowed this bonfire to progress to the stage, where residents are living in fear for the safety of their homes.
"The Minister for Regional Development (Danny Kennedy) must take action to make the area safe and show greater leadership on this issue."
A Northern Ireland Fire and Rescue Service (NIFRS) spokesman stressed that it did not have any enforcement powers in relation to the size or location of bonfires.
He said the service provided safety advice.
"NIFRS continue to work closely with local communities and with the other statutory agencies to ensure people stay safe when building and attending bonfires," he added.
"NIFRS priority is to protect life and secondly property and if NIFRS is called out a bonfire related incident it is because someone from the local community is concerned and has called NIFRS for assistance."
A spokesman for the Department of Regional Development's TransportNI said around 54 homes had been boarded up at the cost of £10,000 as a "precautionary measure".
"The Department does not approve of or support the unauthorised use of its property and its land, including public highways, walkways, and verges," he said.
"Bonfire management is dealt with on an inter-agency basis including, PSNI, Fire Service, local council, community representatives and other stakeholders including TransportNI.
"The Department remains actively engaged with partner stakeholders in efforts to achieve an amicable outcome."
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