In an interview with Premier Christianity magazine, Chan said large churches require a huge amount of money to run Sunday services, but the "LGBT agenda" could jeopardise the tax breaks which thousands of churches and Christian organisations currently receive, thereby making expensive services untenable.
"Do you realise how volatile our system is of our church gatherings? How much money it requires? All it takes is one law that changes the tax breaks that we get and so many churches would have to shut their doors. And when you look at the LGBT agenda, and whatever else is going on in the government, you just think: 'How can I continue with this system that is so dependent on so much money and so many breaks from the government?'
"That can't be the future. Too much has changed."
While Chan said he didn't know if persecution would happen, he warned "it certainly seems like it's headed in that direction".
In his latest book Letters to the Church, Chan makes the case for smaller churches where Christians meets in one another's homes and there's no need to purchase expensive buildings.
"The great movements around the world are not from one person preaching to thousands but by mobilising hundreds and thousands of believers to trust the word of God and trust the Holy Spirit," he says.
The leader, who quit pastoring the megachurch he founded after becoming disillusioned with what he saw, is now an advocate for smaller gatherings.
"Scripture says that every believer has a 'manifestation of the Spirit...for the common good', and so as a leader I need to mobilise that type of power, and we just found that it works better in smaller expressions – because how can we all do that if there's 1,000 people in the room?"
Read the full interview in the February issue of Premier Christianity magazine. Request a free copy here