Mr Phillips, head of the Equality and Human Rights Commission, also claimed that Muslims were making more of an effort to integrate into "modern" society.
He said there was "an awful lot of noise" about the church being persecuted in Britain but contended this was being driven largely by African-Caribbean Christians who "believe in an old-time religion which, in my view, is incompatible with a modern, multi-ethnic, multicultural society".
In contrast, Mr Phillips claimed that Muslim communities in Britain were "doing their damnedest to come to terms with their neighbours to try to integrate and they're doing their best to try to develop an idea of Islam that is compatible with living in a modern liberal democracy".
He said that the real victim of religious discrimination in Britain was more likely to be a Muslim, while "the person most likely to feel slighted because of their religion is an evangelical Christian".
There has been a series of high profile court cases and disciplinary hearings in recent years involving Christians who expressed their faith or followed their consciences, particularly in the workplace.
The cases have led to strong criticism of the Equality Laws by Christians.
In a statement, the Evangelical Alliance (EA) said Mr Phillips was mistaken in assuming Muslims had integrated better into the new world of equality and human rights than Christians.
"The likely reality is that Christianity is seen as a 'soft target'," it said.
The EA criticised Mr Phillips for his "patronising and disparaging" insinuation that African-Caribbean Christian was an irrelevant "old time religion".
"Sadly Mr Phillips fails to appreciate that this expression of Christian belief is at the heart of the mainstream, historic and orthodox Christian church that is growing rapidly in every continent," it said.
Although it insisted Christians were not looking for exceptional treatment, the EA said the Commission had failed to step in when they faced discrimination.
It was not so much secular humanists making Christians feel under siege as "governments and bodies like the Commission that buy into their narrow secularising agenda by pursuing policies that directly and indirectly marginalise people of faith".
Dr Don Horrocks, head of public affairs at the EA said: "Christians have been at the forefront of defending religious liberty and freedom of speech and conscience against the encroachment of a largely secular agenda that has been forcibly seeking to impose a 'one size fits all' blunt instrument of equalities legislation on everyone.
"Such an approach ignorantly assumes that faith adherents can simply suspend their convictions and consciences in public life and keep them private."
The EA urged the Commission to adopt a robust early intervention approach to prevent more cases of religious discrimination from coming before the courts, and told it to "rise to the challenge" of preventing the marginalisation of people of faith from public life.
"While there have been some instances in which Christians have too quickly rushed to court to claim victim status, such 'militancy' may well be a result of the Commission's failure to engage with them," the EA said.
"This failure to engage may have largely destroyed the Commission's own credibility with the faith sector not least by actively taking sides against them, and forced hard-pressed Christians to feel they have no option but to defend themselves.
"However, this must not obscure the fact that there have been many genuine cases in which religious liberty has been unfairly restricted, for example in the areas of freedom of speech and the workplace."
Dr Horrocks added: "If things continue as they are, the time may come when we see more Christians and people of other faiths clogging up our courts and prisons which surely is something that no one wants to see."