CSW first applied for consultative status with the UN's Economic and Social Council (ECOSOC) in 2009.
The status would give CSW access to speak and participate in meetings at key human rights advocacy platforms including the Human Rights Council and General Assembly.
It would also allow the charity to bring people facing persecution into the UN to address policy makers who could make a difference in their country.
The UN NGO committee voted 11-4 against CSW, with one abstention and three absent, to deny CSW's application.
How the committee voted
For: USA, Greece, Uruguay and Israel
Against: China, Cuba, Pakistan, South Africa, Iran, Sudan, Turkey, Venezuela, Nicaragua and India.
Abstain: Russia
Absent: Azerbaijan, Guinea and Mauritania
States that voted against CSW's application included China, Sudan and India - all countries with track records of persecution against Christians.
CSW recently called on China to end the use of torture against prisoners and end human rights abuses against Christians.
Speaking on Premier News Hour, Kiri Kankhwende from CSW said that they will not be silenced by the countries that have opposed them.
She told Premier: "A lot of [these countries] are dead set against us but we're not going to silence our voice in criticising them either."
The NGO Committee members had deferred CSW's application since 2009, asking more than 80 questions regarding their work.
CSW said despite answering the questions in a comprehensive manner the application continued to be deferred, hampering CSW's opportunities to promote the right to freedom of religion.
The UK Mission to the UN will be appealing the decision to the body that oversees the NGO Committee.
CSW's Chief Executive Mervyn Thomas said: "We believe that this decision is effectively an attempt to silence CSW and undermine the promotion of freedom of religion or belief within the UN system.
"We are deeply grateful for the Permanent Missions of the Greece, Israel, Uruguay and the US, who voted to support our application.
"We also warmly welcome the support of the UK Mission to the UN and their intention to appeal this decision."
Kiri Kankhwende told Premier that the charity is hopeful that when their case is brought before the wider committee they stand a better chance of receiving the consultative status.
"We're hopeful that on the wider committee we only have to get about 56 per cent voting in favour so we're going to lobby hard, we're going to pray that we're going to succeed this time."
Listen to Antony Bushfield speaking to Kiri Kankhwende here: