It is believed the demolitions and burning of places of worship are part of a wider attempt to enforce Islamic rule in the nation.
BosNewsLife has reported that two pastors of the Sudan Church of Christ (SCOC) have been detained.
It is thought that the pastors were taken from their homes in North Khartoum in early December and have been named as Kowa Shamaal, the SCOC head of missions, and Hassan Abdelrahim, a SCOC vice moderator.
Christians in the region also reported the arrest of a Christian activist from the Evangelical church, Talahon Nigosi Kassa Ratta.
Allegedly security officials ransacked his home, confiscating a laptop and phone, it was then reported that he was instructed to collect his phone but upon his arrival, was detained.
No charges have yet been brought against him.
Advocacy group, International Christian Concern (ICC) has spoken out, and said that 2015 witnessed: "church demolitions and burnings, arbitrary arrests, and land grabs the state has perpetrated against Christians in a country that both protects religious freedom in its constitution under law, but imposes Islamic sharia law and subjugates religious minorities in practice."
It continued: "President Omar al-Bashir's government maintains a deplorable history persecuting Christians, especially since South Sudan seceded in 2011."