Neville Kyrke-Smith, national director of Aid to the Church in Need (UK), said the Foreign and Commonwealth Office 2012 Report on Human Rights and Democracy published last week "downplays the scale of Christian persecution".
Although he praised the FCO for considering religious freedom issues in its report, he criticised the coverage of intolerance towards Christians.
He highlighted the exodus of Christians from the Middle East, especially Iraq, describing the report's references to this as "woefully inadequate".
Mr Kyrke-Smith said: "While the report describes attacks on members of the Iraq's LGBT community and Emos, it is virtually silent about the various attacks on Christians."
Noting that up to three quarters of Christians have fled Iraq, he added: "Perhaps there are so few left in the country after repeated attacks and bombings that they are no longer seen as significant."
Referring to research showing that 75 per cent of all religious hatred in the world is directed against Christians, Mr Kyrke-Smith said: "The FCO must not gloss over the problems faced [by Christians] in these countries, leaving serious cases of religious hatred unacknowledged and unmentioned.
"It must make sure that the voices of all persecuted groups are heard and responded to."
Mr Kyrke-Smith cited research showing that 200 million Christians face discrimination or persecution and other reports that at least 100,000 are killed for their Christian faith every year.
He expressed particular concern that the problems faced by Christian women in many countries were given little or no coverage.
While the FCO report mentions the problem of Coptic Christians girls being abducted and forced to convert in Egypt, he said: "there seems to be no realisation of the scale of the abductions".
He referred to evidence given at the US Helsinki Commission in 2011, which stated that up to 800 Coptic Christian women have been kidnapped since 2009.
Similarly Mr Kyrke-Smith expressed concern that there was no mention of the problems facing Christian women in Pakistan.
He said: "Women from religious minorities [in Pakistan] are more likely to experience sexual harassment or be raped, so it was particularly distressing to find this aspect entirely overlooked.
"To give just one, heart-rending, example, in March 2012, a 14 year old Christian girl was repeatedly raped by a policeman at gun point, while her grandparents were bound and gagged in the next room.
"These pressing and critical issues should have found space in the FCO report – but they did not."
Noting the absence of any reference to China's "underground" Catholic clergy in detention or the seizure of property belonging to Three-Self Patriotic Movement, set up for Protestant Christians, he said there were "gaps in the authors' knowledge".
He added: "While welcoming the FCO's commitment to 'constructive long-term engagement' and 'detailed expert discussions on the role of faith groups in civil society' in China – these are no substitute for directly addressing the range of problems faced by Christians."
Mr Kyrke-Smith concluded: "Sometimes we are not always aware of the scale of the problem in the West, as some Christian communities are afraid to speak out about the reality as it could make matters worse."
"But that means that those of us in the West who are aware of their suffering have a moral responsibility to do so on their behalf and highlight the dangers to and suffering of some communities."