Tweeting an apology on Wednesday, President Akufo-Addo said it was regrettable that such an incident had taken place in his country.
Last weekend a group of armed men infiltrated the compound with a bulldozer, pulling down buildings which were under construction.
Several arrests have been made in connection with the incident with several suspects charged with unlawful entry and causing unlawful damage.
The Nigerian High Commission in Accra in a statement accused a Ghanaian businessman who was disputing onwership of the land as the main architect of the demolition exercise.
On Monday, Nigerians living in Ghana staged a demonstration demanding an immediate investigation.
Under the “Nigerian Lives Matter” slogan, they accused Ghanaians of open provocation and sabotage to their businesses in Ghana.
Days ago Nigeria's Foreign Affairs Minister Geoffrey Onyeama had summoned a senior Ghanaian diplomat in Abuja over the demolition which took place on 19 June.