Andrew Boyd, a spokesperson from Release International told Premier: "The typical cross on a Chinese church is bright red but the authorities in some areas have been saying, 'You've got to pull that down, you've got to replace that with a Chinese flag'.
"And we've seen over the past few years there's been a campaign of cross removals taking place."
The religious freedoms organisation said the situation has got worse since the new legislation, which gives authorities more say over what churches can do and whether they can even exist.
It claimed more churches are being driven underground as a result.
Boyd told Premier the Chinese authorities feel threatened by Christianity.
"The number of Christians within China now outnumbers members of the Communist party. China is heading towards being the most Christianised nation on earth, which is really extraordinary.
"And the authorities are deeply concerned about this so they are tightening up on their regulations and tightening up on the Church...but that's the good news - that the Church is growing!"
The Christian organisation has launched an online petition for the attention of China's President Xi Jinping that will end 31st October.
Listen to Andrew Boyd speaking with Premier's Cara Bentley:
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.