Christian Solidarity Worldwide (CSW) said the sanctuary, two offices and a centre used for Sunday school at Sudan Church of Christ (SCOC) in Soba Aradi were destroyed on 7th May without any notice from Khartoum State authorities.
The church was one of 27 churches fighting a joint case against a government decision to confiscate and demolish their buildings.
According to CSW, the Administrative Court recently decided to dismiss the case, but the judge had not delivered his written decision, which prevented the churches' lawyers from appealing the decision.
CSW said church members living close to the church rushed to the scene when the church was being demolished, but were prevented from taking photos or filming.
The charity stated: "They were also ordered to unlock parts of the building to assist the demolition process.
"After refusing to comply with these orders, two men, Boulus Salih and Nagi Abdallah, were detained by NISS officers and interrogated for two hours.
"They were released after being forced to sign a document stating that they would not take photos of the demolished building."
Church members held a prayer service next to the wrecked building once the demolition was complete.
CSW's Chief Executive Mervyn Thomas said: "We are dismayed to hear of the destruction of yet another church in Khartoum.
"It is alarming that the demolition took place without due process and on the day the church holds its main weekly service.
"Whilst the government continues to present these cases as a purely administrative matter, the fact remains that the destruction of houses of worship violates all international norms, as does the use of excessive force on civilians who are peaceably exercising their right to worship in communion with others.
"We urge the government to review the current demolition orders to ensure that they comply with Sudan's domestic and international human rights obligations."
CSW said twelve churches have been demolished since 2011 in Soba Aradi due to a government planning and re-development programme.
The church congregation will not be able to repair or replace the building because the law has banned issuing permits for the construction of new church buildings.