A Ghanaian businessman had accused the commission of encroaching on his land.
He was said to have visited the property penultimate week, presenting evidence that he was the real owner of the land.
However, he reportedly returned to the site on Friday in the company of armed men who supervised the demolition.
Officials of the commission reportedly contacted the police but efforts were not made to prevent the demolition.
The Nigerian and Ghanaian authorities have yet to react to the issue, which comes five months after the Ministry of Foreign Affairs denied reports that the Nigerian commission in Ghana had been evicted in Accra.
The spokesperson for the ministry, Ferdinand Nwonye, in a statement, had said there was no “diplomatic row between Nigeria and the Republic of Ghana.”
Nwonye had said though the lease of the property on No.10 Barnes Road, Accra, has expired, the high commission was exploring the possibility of renewing the lease agreement with the host authorities.