Commissioner of the GRA Kofi Nti argued that the move was necessary because such activities fall out of the legal remit of the churches' operation across the country.
He said the Authority will soon conduct investigations into activities of all churches in the country with the view to taxing them based on their level of business transactions.
Meanwhile, President Nana Addo Dankwa Akufo-Addo has backed calls for churches in the country to be taxed.
According to him, the debate on taxing churches came up because of the affluence being displayed by some members of the clergy.
He said "The public looks on as some of the churches appear to forget about the poor and venerable in society and concentrate on being outrageous.
"It is not surprising that there are calls for taxes to be imposed on church incomes. When you step out of the charity sphere, out of education and out of healthcare, you are putting yourself in the line of the tax net."