It has questioned the millions of pounds in aid being sent to the likes of Eritrea, Sudan and Pakistan where Christians are experiencing hardship and discrimination because of their faith.
In Eritrea, which received over £3million during the last financial year, Christians are being detained in metal shipping containers and tortured in order to make them recant their faith.
Sudan received over £32million in aid last year, but Barnabas Fund describes the government as an "extreme persecutor" of Christians. The organisation has been evacuating thousands of Christian women and children in the face of growing hostility.
Christians continue to experience persecution in Pakistan as a result of the blasphemy laws, which are being misused by extremists. False accusations have led to attacks, lengthy imprisonments, and death sentences, although no one has yet been executed for the offence.
Christian women also face abduction by Muslim men, who force them to convert to Islam and marry them. Christians complain that little is done to prevent these injustices and perpetrators often escape justice.
Despite these human rights abuses, Pakistan received over £211million in aid from the UK Government last year.
In a response to Barnabas Fund's concerns, the Department for International Development said it "robustly assesses" the suitability of governments receiving aid and that respecting human rights is one of the factors taken into consideration.
"We may judge that specific human rights concerns are sufficiently serious to merit a suspension of our financial aid to that government," DFID said.
"If financial aid is suspended, we make sure those funds are provided in alternative ways so that the poorest do not suffer as a result."
Barnabas Fund said that the total withdrawal of UK aid from a country where Christians are being persecuted could make things worse for the most disadvantaged.
"Yet propping up regimes that abuse their most vulnerable citizens hardly encourages change", it added.
"While the UK Government pays lip service to the importance of human rights, it is questionable whether it is truly putting its money where its mouth is in the payment of aid to countries that persecute Christians."