Making the announcement last week, Al-Fatih Taj El-sir said there was a lack of worshippers in the country and a rise in the number of abandoned church buildings.
According to Christian Solidarity Worldwide (CSW), he claimed there was no need for new churches whilst maintaining that there was still freedom to worship in Sudan.
Despite his claims, CSW said there had been a "campaign of repression" against Christians in northern Sudan since last December. This includes arrests, detentions and the deportation of Christians, particularly in Sudan's two largest cities, Khartoum and Omodorum.
The Catholic Information Service for Africa (CISA) reports that a senior South Sudanese Catholic priest, Father Maurino, and two expatriate missionaries were deported on 12 April.
The two missionaries, one from France and the other from Egypt, worked with children in Khartoum.
Fr Maurino said no reason had been given for the deportations. He is concerned that the Sudanese government is attempting to eliminate Christians from the country.
CSW also reports the "systematic targeting" of members of African ethnic groups, particularly the Nuba, giving rise to concerns about the Islamisation and Arabisation of Sudan.
"The campaign of repression [has] continued into 2013, with foreign Christians being arrested and deported at short notice, and those from Sudan facing arrest, detention and questioning by the security services, as well as the confiscation of property such as mobile phones, identity cards and laptops. In addition to the arrests and deportations, local reports cite a media campaign warning against 'Christianisation'," said CSW.
The organisation said the minister's claims of freedom to worship were at odds with reports of repression.
In February, at least 55 Christians linked to the Evangelical Church in Khartoum are reported to have been detained without charge.
On 18 February, the cultural centre of the Sudan Presbyterian Evangelical Church (SPEC) in Khartoum was raided by the National Intelligence and Security Services (NISS).
Three people were arrested at the premises and several items were confiscated, including books and media equipment. The three arrested were all from South Sudan. One was released days after the initial arrest.
CSW's Advocacy Director Andrew Johnston said, "The recent spike in religious repression in Sudan is deeply worrying.
"The minister's claims of guaranteeing freedom to worship are at odds with regular reports of Christians being harassed arrested and in some cases expelled from the country at short notice.
"We urge the Sudanese government to end its campaign of harassment against the Christian community and respect the right of all of its citizens to freedom of religion or belief, as outlined in Article 18 of the International Covenant on Civil and Political Rights (ICCPR), to which Sudan is a signatory."